1DO8 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME

Authors :   Z. Yang, D. L. Floyd, G. Loeber, L. Tong

Date :   19 Dec 99 (Deposition) - 06 Mar 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Oxidative Decarboxylase, Four Domains: One With Rossmann Fold, One With Parallel Alpha-Beta Fold, One Mostly Helical, And One Mostly Extended, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Yang, D. L. Floyd, G. Loeber, L. Tong
Structure Of A Closed Form Of Human Malic Enzyme And Implications For Catalytic Mechanism.
Nat. Struct. Biol. V. 7 251 2000
PubMed-ID: 10700286 | Reference-DOI: 10.1038/73378
(for further references see the PDB file header)

Molecule 1 - MALIC ENZYME
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.39
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRH281
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 72)

No.	Name	Count	Type	Full Name
1	MN	4	Ligand/Ion	MANGANESE (II) ION
2	MSE	56	Mod. Amino Acid	SELENOMETHIONINE
3	NAD	8	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	OXL	4	Ligand/Ion	OXALATE ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:112 , ARG A:165 , LEU A:167 , LYS A:183 , GLU A:255 , ASP A:256 , ASP A:279 , ASN A:421 , ASN A:466 , ASN A:467 , NAD A:601 , MN A:604 , HOH A:4290	BINDING SITE FOR RESIDUE OXL A 603
02	AC2	SOFTWARE	ARG A:165 , GLU A:255 , ASP A:256 , ASP A:279 , OXL A:603 , HOH A:606	BINDING SITE FOR RESIDUE MN A 604
03	AC3	SOFTWARE	ARG B:1165 , LEU B:1167 , LYS B:1183 , GLU B:1255 , ASP B:1256 , ASP B:1279 , ASN B:1421 , ASN B:1466 , ASN B:1467 , NAD B:1601 , MN B:1604 , HOH B:4112	BINDING SITE FOR RESIDUE OXL B 1603
04	AC4	SOFTWARE	ARG B:1165 , GLU B:1255 , ASP B:1256 , ASP B:1279 , OXL B:1603 , HOH B:1606	BINDING SITE FOR RESIDUE MN B 1604
05	AC5	SOFTWARE	ARG C:2165 , LEU C:2167 , LYS C:2183 , GLU C:2255 , ASP C:2256 , ASP C:2279 , ASN C:2421 , ASN C:2466 , ASN C:2467 , NAD C:2601 , MN C:2604 , HOH C:4054	BINDING SITE FOR RESIDUE OXL C 2603
06	AC6	SOFTWARE	ARG C:2165 , GLU C:2255 , ASP C:2256 , ASP C:2279 , OXL C:2603 , HOH C:2606	BINDING SITE FOR RESIDUE MN C 2604
07	AC7	SOFTWARE	ARG D:3165 , LEU D:3167 , LYS D:3183 , GLU D:3255 , ASP D:3256 , ASP D:3279 , ASN D:3421 , ASN D:3466 , ASN D:3467 , NAD D:3601 , MN D:3604 , HOH D:4119	BINDING SITE FOR RESIDUE OXL D 3603
08	AC8	SOFTWARE	ARG D:3165 , GLU D:3255 , ASP D:3256 , ASP D:3279 , OXL D:3603 , HOH D:3606	BINDING SITE FOR RESIDUE MN D 3604
09	AC9	SOFTWARE	ARG A:165 , LEU A:167 , GLY A:168 , ASN A:259 , ASP A:279 , THR A:283 , GLY A:311 , ALA A:312 , GLY A:313 , GLU A:314 , ALA A:315 , ASP A:345 , LYS A:346 , VAL A:392 , ALA A:393 , GLY A:394 , ALA A:395 , LEU A:398 , LEU A:419 , ASN A:421 , GLY A:446 , GLY A:465 , ASN A:466 , ASN A:467 , OXL A:603 , HOH A:4007 , HOH A:4315	BINDING SITE FOR RESIDUE NAD A 601
10	BC1	SOFTWARE	HIS A:154 , ARG A:194 , ARG A:197 , ILE A:479 , LEU A:480 , ARG A:542 , TYR A:552 , ARG A:556 , HOH A:4739 , HOH A:4888 , ASP D:3244 , ARG D:3245 , GLY D:3247	BINDING SITE FOR RESIDUE NAD A 602
11	BC2	SOFTWARE	ARG B:1165 , LEU B:1167 , GLY B:1168 , ASN B:1259 , THR B:1283 , GLY B:1311 , ALA B:1312 , GLY B:1313 , GLU B:1314 , ALA B:1315 , ASP B:1345 , LYS B:1346 , VAL B:1392 , ALA B:1393 , GLY B:1394 , LEU B:1398 , LEU B:1419 , ASN B:1421 , GLY B:1446 , GLY B:1465 , ASN B:1466 , ASN B:1467 , OXL B:1603 , HOH B:4066 , HOH B:4933	BINDING SITE FOR RESIDUE NAD B 1601
12	BC3	SOFTWARE	HIS B:1154 , LYS B:1156 , GLY B:1192 , ARG B:1194 , ARG B:1197 , ILE B:1479 , LEU B:1480 , ARG B:1542 , ARG B:1556 , HOH B:4443 , ARG C:2245	BINDING SITE FOR RESIDUE NAD B 1602
13	BC4	SOFTWARE	ARG C:2165 , LEU C:2167 , GLY C:2168 , ASN C:2259 , ASP C:2279 , THR C:2283 , GLY C:2311 , ALA C:2312 , GLY C:2313 , GLU C:2314 , ALA C:2315 , ASP C:2345 , LYS C:2346 , VAL C:2392 , ALA C:2393 , GLY C:2394 , ALA C:2395 , LEU C:2419 , ASN C:2421 , GLY C:2446 , GLY C:2465 , ASN C:2466 , ASN C:2467 , OXL C:2603 , HOH C:4017 , HOH C:4175 , HOH C:4678	BINDING SITE FOR RESIDUE NAD C 2601
14	BC5	SOFTWARE	ARG B:1245 , HOH B:4632 , HIS C:2154 , LYS C:2156 , GLY C:2192 , ILE C:2193 , ARG C:2194 , ARG C:2197 , ILE C:2479 , LEU C:2480 , ARG C:2542 , TYR C:2552 , ARG C:2556 , HOH C:4303	BINDING SITE FOR RESIDUE NAD C 2602
15	BC6	SOFTWARE	ARG D:3165 , LEU D:3167 , GLY D:3168 , ASN D:3259 , ASP D:3279 , THR D:3283 , GLY D:3311 , ALA D:3312 , GLY D:3313 , GLU D:3314 , ALA D:3315 , ASP D:3345 , LYS D:3346 , VAL D:3392 , ALA D:3393 , GLY D:3394 , ALA D:3395 , LEU D:3398 , LEU D:3419 , ASN D:3421 , GLY D:3446 , GLY D:3465 , ASN D:3466 , ASN D:3467 , OXL D:3603 , HOH D:4124 , HOH D:4485 , HOH D:4533 , HOH D:4788	BINDING SITE FOR RESIDUE NAD D 3601
16	BC7	SOFTWARE	ASP A:244 , ARG A:245 , HIS D:3154 , ARG D:3194 , ARG D:3197 , ILE D:3479 , LEU D:3480 , ASN D:3482 , ARG D:3542 , TYR D:3552 , ARG D:3556	BINDING SITE FOR RESIDUE NAD D 3602

(no "SS Bond" information available for 1DO8)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:113	-	Pro A:114
2	Asn A:421	-	Pro A:422
3	Tyr A:543	-	Pro A:544
4	Thr B:1113	-	Pro B:1114
5	Asn B:1421	-	Pro B:1422
6	Tyr B:1543	-	Pro B:1544
7	Thr C:2113	-	Pro C:2114
8	Asn C:2421	-	Pro C:2422
9	Tyr C:2543	-	Pro C:2544
10	Thr D:3113	-	Pro D:3114
11	Asn D:3421	-	Pro D:3422
12	Tyr D:3543	-	Pro D:3544

Asymmetric/Biological Unit (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034104	P	114	L	MAOM_HUMAN	Polymorphism	16952692	A B C D	P	114 1114 2114 3114	L
2	UniProt	VAR_050017	G	450	E	MAOM_HUMAN	Polymorphism	649224	A B C D	G	450 1450 2450 3450	E

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MALIC_ENZYMES	PS00331	Malic enzymes signature.	MAOM_HUMAN	276-292	4	A:276-292 B:1276-1292 C:2276-2292 D:3276-3292

Asymmetric/Biological Unit (15, 60)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000321341	1a	ENSE00001948888	chr18:48405419-48405678	260	MAOM_HUMAN	-	0	0	-	-
1.2	ENST00000321341	2	ENSE00001222938	chr18:48422179-48422298	120	MAOM_HUMAN	1-36	36	4	A:21-36 B:1021-1036 C:2021-2036 D:3021-3036	16 16 16 16
1.3	ENST00000321341	3	ENSE00000996845	chr18:48434433-48434566	134	MAOM_HUMAN	37-81	45	4	A:37-81 B:1037-1081 C:2037-2081 D:3037-3081	45 45 45 45
1.4	ENST00000321341	4	ENSE00000996846	chr18:48439171-48439320	150	MAOM_HUMAN	81-131	51	4	A:81-131 B:1081-1131 C:2081-2131 D:3081-3131	51 51 51 51
1.5	ENST00000321341	5	ENSE00001151659	chr18:48442538-48442613	76	MAOM_HUMAN	131-156	26	4	A:131-156 B:1131-1156 C:2131-2156 D:3131-3156	26 26 26 26
1.6	ENST00000321341	6	ENSE00001151654	chr18:48443717-48443878	162	MAOM_HUMAN	157-210	54	4	A:157-210 B:1157-1210 C:2157-2210 D:3157-3210	54 54 54 54
1.7	ENST00000321341	7	ENSE00001151650	chr18:48444480-48444583	104	MAOM_HUMAN	211-245	35	4	A:211-245 B:1211-1245 C:2211-2245 D:3211-3245	35 35 35 35
1.8	ENST00000321341	8	ENSE00001151645	chr18:48446826-48446935	110	MAOM_HUMAN	245-282	38	4	A:245-282 B:1245-1282 C:2245-2282 D:3245-3282	38 38 38 38
1.9	ENST00000321341	9	ENSE00001151639	chr18:48447031-48447128	98	MAOM_HUMAN	282-314	33	4	A:282-314 B:1282-1314 C:2282-2314 D:3282-3314	33 33 33 33
1.10	ENST00000321341	10	ENSE00001151634	chr18:48447444-48447557	114	MAOM_HUMAN	315-352	38	4	A:315-352 B:1315-1352 C:2315-2352 D:3315-3352	38 38 38 38
1.11	ENST00000321341	11	ENSE00000950181	chr18:48450468-48450582	115	MAOM_HUMAN	353-391	39	4	A:353-391 B:1353-1391 C:2353-2391 D:3353-3391	39 39 39 39
1.12	ENST00000321341	12	ENSE00000950182	chr18:48452126-48452268	143	MAOM_HUMAN	391-438	48	4	A:391-438 B:1391-1438 C:2391-2438 D:3391-3438	48 48 48 48
1.13	ENST00000321341	13	ENSE00000950183	chr18:48458628-48458730	103	MAOM_HUMAN	439-473	35	4	A:439-473 B:1439-1473 C:2439-2473 D:3439-3473	35 35 35 35
1.14	ENST00000321341	14	ENSE00000950184	chr18:48465940-48466010	71	MAOM_HUMAN	473-496	24	4	A:473-496 B:1473-1496 C:2473-2496 D:3473-3496	24 24 24 24
1.15	ENST00000321341	15	ENSE00000950185	chr18:48466658-48466756	99	MAOM_HUMAN	497-529	33	4	A:497-529 B:1497-1529 C:2497-2529 D:3497-3529	33 33 33 33
1.16b	ENST00000321341	16b	ENSE00001605064	chr18:48473387-48474691	1305	MAOM_HUMAN	530-584	55	4	A:530-573 B:1530-1573 C:2530-2573 D:3530-3573	44 44 44 44

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:553
 aligned with MAOM_HUMAN | P23368 from UniProtKB/Swiss-Prot  Length:584

    Alignment length:553
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570   
          MAOM_HUMAN     21 IKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHRNLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMGLYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEVSINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP  573
               SCOP domains d1do8a2 A:21-279 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                       d1do8a1 A:280-573 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1do8A01 A:21-277 Aminoacid dehydrogenase-like, N-terminal domain. Chain A                                                                                                                                                                                        1do8A02 A:278-573 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh....hhhhhhhhhhhhh...........hhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eeee.hhh.hhhhhhh........eeeee..........hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee....hhhhhh.............hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee..hhhhhhhhhhhhhhhhh...hhhhhhh.eeeee..ee............hhhhh.........hhhhhhhhhh..eeee........hhhhhhhhhhhh...eeee...hhhhh..hhhhhhhhh....eeee......ee.....ee..ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MALIC_ENZYMES    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        Exon 1.3  PDB: A:37-81 UniProt: 37-81        -------------------------------------------------Exon 1.5  PDB: A:131-156  Exon 1.6  PDB: A:157-210 UniProt: 157-210             Exon 1.7  PDB: A:211-245           ------------------------------------Exon 1.9  PDB: A:282-314         Exon 1.10  PDB: A:315-352             Exon 1.11  PDB: A:353-391              -----------------------------------------------Exon 1.13  PDB: A:439-473          -----------------------Exon 1.15  PDB: A:497-529        Exon 1.16b  PDB: A:530-573 UniProt: 530-584  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------Exon 1.4  PDB: A:81-131 UniProt: 81-131            -----------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:245-282              ------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:391-438 UniProt: 391-438      ----------------------------------Exon 1.14  PDB: A:473-49----------------------------------------------------------------------------- Transcript 1 (2)
                1do8 A   21 IKEKGKPLmLNPRTNKGmAFTLQERQmLGLQGLLPPKIETQDIQALRFHRNLKKmTSPLEKYIYImGIQERNEKLFYRILQDDIESLmPIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGmGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYmGLYQKRDRTQQYDDLIDEFmKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVmSmVENGLSEQEAQKKIWmFDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAmASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEVSINIAIKVTEYLYANKmAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP  573
                                    30       |40      | 50        60        70    |   80     |  90       100       110       120       130       140       150       160       170      |180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    | |330       340  |    350       360       370       380       390       400      |410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570   
                                   29-MSE   38-MSE   47-MSE                      75-MSE     86-MSE               108-MSE                                                              177-MSE                                   219-MSE             239-MSE                                                                               325-MSE           343-MSE                                                         407-MSE                                                                                                                             539-MSE                              
                                                                                                                                                                                                                                                                                                                                            327-MSE

Chain B from PDB  Type:PROTEIN  Length:553
 aligned with MAOM_HUMAN | P23368 from UniProtKB/Swiss-Prot  Length:584

    Alignment length:553
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570   
          MAOM_HUMAN     21 IKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHRNLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMGLYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEVSINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP  573
               SCOP domains d1do8b4 B:1021-1279 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                    d1do8b3 B:1280-1573 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1do8B01 B:1021-1277 Aminoacid dehydrogenase-like, N-terminal domain. Chain A                                                                                                                                                                                     1do8B02 B:1278-1573 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh....hhhhhhhhhhhhh...........hhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eeee.hhh.hhhhhhh........eeeee..........hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee......hhhhh............hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee..hhhhhhhhhhhhhhhhhh..hhhhhhhheeeee..ee............hhhhh.........hhhhhhhhhh..eeee........hhhhhhhhhhhh...eeee...hhhhh..hhhhhhhhh....eeee......ee.....ee..ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MALIC_ENZYMES    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        Exon 1.3  PDB: B:1037-1081 UniProt: 37-81    -------------------------------------------------Exon 1.5  PDB: B:1131-1156Exon 1.6  PDB: B:1157-1210 UniProt: 157-210           Exon 1.7  PDB: B:1211-1245         ------------------------------------Exon 1.9  PDB: B:1282-1314       Exon 1.10  PDB: B:1315-1352           Exon 1.11  PDB: B:1353-1391            -----------------------------------------------Exon 1.13  PDB: B:1439-1473        -----------------------Exon 1.15  PDB: B:1497-1529      Exon 1.16b  PDB: B:1530-1573 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------Exon 1.4  PDB: B:1081-1131 UniProt: 81-131         -----------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:1245-1282            ------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: B:1391-1438 UniProt: 391-438    ----------------------------------Exon 1.14               ----------------------------------------------------------------------------- Transcript 1 (2)
                1do8 B 1021 IKEKGKPLmLNPRTNKGmAFTLQERQmLGLQGLLPPKIETQDIQALRFHRNLKKmTSPLEKYIYImGIQERNEKLFYRILQDDIESLmPIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGmGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYmGLYQKRDRTQQYDDLIDEFmKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVmSmVENGLSEQEAQKKIWmFDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAmASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEVSINIAIKVTEYLYANKmAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP 1573
                                  1030      1040      1050      1060      1070    | 1080     |1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320    | 1330      1340  |   1350      1360      1370      1380      1390      1400      1410      1420      1430      1440      1450      1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570   
                                 1029-MSE 1038-MSE 1047-MSE                    1075-MSE   1086-MSE              1108-MSE                                                             1177-MSE                                  1219-MSE            1239-MSE                                                                              1325-MSE          1343-MSE                                                        1407-MSE                                                                                                                            1539-MSE                              
                                                                                                                                                                                                                                                                                                                                           1327-MSE

Chain C from PDB  Type:PROTEIN  Length:553
 aligned with MAOM_HUMAN | P23368 from UniProtKB/Swiss-Prot  Length:584

    Alignment length:553
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570   
          MAOM_HUMAN     21 IKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHRNLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMGLYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEVSINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP  573
               SCOP domains d1do8c4 C:2021-2279 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                    d1do8c3 C:2280-2573 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1do8C01 C:2021-2277 Aminoacid dehydrogenase-like, N-terminal domain. Chain A                                                                                                                                                                                     1do8C02 C:2278-2573 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh....hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eeee.hhh.hhhhhhh........eeeee..........hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee....hhhhhh.............hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee..hhhhhhhhhhhhhhhhhh..hhhhhhhheeeee..ee............hhhhh.........hhhhhhhhhh..eeee........hhhhhhhhhhhh...eeee...hhhhh..hhhhhhhhh....eeee......ee.....ee..ee.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MALIC_ENZYMES    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        Exon 1.3  PDB: C:2037-2081 UniProt: 37-81    -------------------------------------------------Exon 1.5  PDB: C:2131-2156Exon 1.6  PDB: C:2157-2210 UniProt: 157-210           Exon 1.7  PDB: C:2211-2245         ------------------------------------Exon 1.9  PDB: C:2282-2314       Exon 1.10  PDB: C:2315-2352           Exon 1.11  PDB: C:2353-2391            -----------------------------------------------Exon 1.13  PDB: C:2439-2473        -----------------------Exon 1.15  PDB: C:2497-2529      Exon 1.16b  PDB: C:2530-2573 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------Exon 1.4  PDB: C:2081-2131 UniProt: 81-131         -----------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: C:2245-2282            ------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: C:2391-2438 UniProt: 391-438    ----------------------------------Exon 1.14               ----------------------------------------------------------------------------- Transcript 1 (2)
                1do8 C 2021 IKEKGKPLmLNPRTNKGmAFTLQERQmLGLQGLLPPKIETQDIQALRFHRNLKKmTSPLEKYIYImGIQERNEKLFYRILQDDIESLmPIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGmGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYmGLYQKRDRTQQYDDLIDEFmKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVmSmVENGLSEQEAQKKIWmFDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAmASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEVSINIAIKVTEYLYANKmAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP 2573
                                  2030      2040      2050      2060      2070    | 2080     |2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210      2220      2230      2240      2250      2260      2270      2280      2290      2300      2310      2320    | 2330      2340  |   2350      2360      2370      2380      2390      2400      2410      2420      2430      2440      2450      2460      2470      2480      2490      2500      2510      2520      2530      2540      2550      2560      2570   
                                 2029-MSE 2038-MSE 2047-MSE                    2075-MSE   2086-MSE              2108-MSE                                                             2177-MSE                                  2219-MSE            2239-MSE                                                                              2325-MSE          2343-MSE                                                        2407-MSE                                                                                                                            2539-MSE                              
                                                                                                                                                                                                                                                                                                                                           2327-MSE

Chain D from PDB  Type:PROTEIN  Length:553
 aligned with MAOM_HUMAN | P23368 from UniProtKB/Swiss-Prot  Length:584

    Alignment length:553
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570   
          MAOM_HUMAN     21 IKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHRNLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMGLYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEVSINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP  573
               SCOP domains d1do8d4 D:3021-3279 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                    d1do8d3 D:3280-3573 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1do8D01 D:3021-3277 Aminoacid dehydrogenase-like, N-terminal domain. Chain A                                                                                                                                                                                     1do8D02 D:3278-3573 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh....hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eeee.hhh.hhhhhhh........eeeee..........hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee....hhhhhh.............hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhh.hhhhh.eeee..hhhhhhhhhhhhhhhhh...hhhhhhh.eeeee..ee............hhhhh.........hhhhhhhhhh..eeee........hhhhhhhhhhhh...eeee...hhhhh..hhhhhhhhhh...eeee......ee.....ee..ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------L-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MALIC_ENZYMES    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        Exon 1.3  PDB: D:3037-3081 UniProt: 37-81    -------------------------------------------------Exon 1.5  PDB: D:3131-3156Exon 1.6  PDB: D:3157-3210 UniProt: 157-210           Exon 1.7  PDB: D:3211-3245         ------------------------------------Exon 1.9  PDB: D:3282-3314       Exon 1.10  PDB: D:3315-3352           Exon 1.11  PDB: D:3353-3391            -----------------------------------------------Exon 1.13  PDB: D:3439-3473        -----------------------Exon 1.15  PDB: D:3497-3529      Exon 1.16b  PDB: D:3530-3573 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------Exon 1.4  PDB: D:3081-3131 UniProt: 81-131         -----------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: D:3245-3282            ------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: D:3391-3438 UniProt: 391-438    ----------------------------------Exon 1.14               ----------------------------------------------------------------------------- Transcript 1 (2)
                1do8 D 3021 IKEKGKPLmLNPRTNKGmAFTLQERQmLGLQGLLPPKIETQDIQALRFHRNLKKmTSPLEKYIYImGIQERNEKLFYRILQDDIESLmPIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGmGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYmGLYQKRDRTQQYDDLIDEFmKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVmSmVENGLSEQEAQKKIWmFDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAmASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEVSINIAIKVTEYLYANKmAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP 3573
                                  3030      3040      3050      3060      3070    | 3080     |3090      3100      3110      3120      3130      3140      3150      3160      3170      3180      3190      3200      3210      3220      3230      3240      3250      3260      3270      3280      3290      3300      3310      3320    | 3330      3340  |   3350      3360      3370      3380      3390      3400      3410      3420      3430      3440      3450      3460      3470      3480      3490      3500      3510      3520      3530      3540      3550      3560      3570   
                                 3029-MSE 3038-MSE 3047-MSE                    3075-MSE   3086-MSE              3108-MSE                                                             3177-MSE                                  3219-MSE            3239-MSE                                                                              3325-MSE          3343-MSE                                                        3407-MSE                                                                                                                            3539-MSE                              
                                                                                                                                                                                                                                                                                                                                           3327-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Aminoacid dehydrogenase-like, N-terminal domain. Chain A (17)

Human (Homo sapiens) (11)

1a	1do8A01	A:21-277
1b	1do8B01	B:1021-1277
1c	1do8C01	C:2021-2277
1d	1do8D01	D:3021-3277

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Human (Homo sapiens) (188)

2a	1do8A02	A:278-573
2b	1do8B02	B:1278-1573
2c	1do8C02	C:2278-2573
2d	1do8D02	D:3278-3573

(no "Pfam Domain" information available for 1DO8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (MAOM_HUMAN | P23368)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0004471	malate dehydrogenase (decarboxylating) (NAD+) activity	Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH + H+.
	GO:0004470	malic enzyme activity	Catalysis of the oxidative decarboxylation of malate with the concomitant production of pyruvate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008948	oxaloacetate decarboxylase activity	Catalysis of the reaction: oxaloacetate = pyruvate + CO2.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0006108	malate metabolic process	The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:1902031	regulation of NADP metabolic process	Any process that modulates the frequency, rate or extent of NADP metabolic process.
cellular component
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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Access by PDB/NDB ID
	1do8
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	MAOM_HUMAN \| P23368
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	1.1.1.39
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UniProtKB/Swiss-Prot
	MAOM_HUMAN \| P23368	:	1efk 1efl 1gz3 1gz4 1pj2 1pj3 1pj4 1pjl 1qr6

1qr6	CRYSTAL STRUCTURE OF AN OPEN FORM OF THE ENZYME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 72)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 8)

PROSITE Motifs (1, 4)

Exons (15, 60)

Sequences/Alignments

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SCOP Domains (2, 8)

CATH Domains (2, 8)

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Gene Ontology (15, 15)

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