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Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN MALATE DEHYDROGENASE TYPE 2

Authors :   E. Ugochukwu, N. Shafqat, A. Rojkova, M. Sundstrom, C. Arrowsmith, J. W A. Edwards, F. Von Delft, U. Oppermann, Structural Genomics Conso (Sgc)

Date :   28 Feb 06 (Deposition) - 28 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Dehydrogenase, Citric Acid Cycle, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ugochukwu, N. Shafqat, A. Rojkova, M. Sundstrom, C. Arrowsmith, J. Weigelt, A. Edwards, F. Von Delft, U. Oppermann
Crystal Structure Of Human Malate Dehydrogenase Type 2
To Be Published
PubMed: search

Molecule 1 - MALATE DEHYDROGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MDH2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MALATE DEHYDROGENASE TYPE 2

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 19)

No.	Name	Count	Type	Full Name
1	ALA	1	Mod. Amino Acid	ALANINE
2	CL	7	Ligand/Ion	CHLORIDE ION
3	HIS	3	Mod. Amino Acid	HISTIDINE
4	MLT	4	Ligand/Ion	MALATE ION
5	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	ALA	1	Mod. Amino Acid	ALANINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	HIS	2	Mod. Amino Acid	HISTIDINE
4	MLT	2	Ligand/Ion	MALATE ION
5	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	ALA	-1	Mod. Amino Acid	ALANINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	HIS	1	Mod. Amino Acid	HISTIDINE
4	MLT	2	Ligand/Ion	MALATE ION
5	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 3 (4, 12)

No.	Name	Count	Type	Full Name
1	ALA	1	Mod. Amino Acid	ALANINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	HIS	3	Mod. Amino Acid	HISTIDINE
4	MLT	4	Ligand/Ion	MALATE ION
5	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG D:86 , ARG D:92 , ASN D:124 , ARG D:158 , HIS D:182 , GLY D:216 , NAD D:3004 , HOH D:3399 , HOH D:3400	BINDING SITE FOR RESIDUE MLT D 3101
02	AC2	SOFTWARE	ARG B:86 , ARG B:92 , ASN B:124 , ARG B:158 , HIS B:182 , GLY B:216 , NAD B:3001 , HOH B:3405 , HOH B:3528	BINDING SITE FOR RESIDUE MLT B 3102
03	AC3	SOFTWARE	ARG C:86 , ARG C:92 , ASN C:124 , ARG C:158 , HIS C:182 , GLY C:216 , ALA C:229 , NAD C:3002 , HOH C:3509 , HOH C:3729	BINDING SITE FOR RESIDUE MLT C 3103
04	AC4	SOFTWARE	ARG A:86 , ARG A:92 , ASN A:124 , ARG A:158 , HIS A:182 , GLY A:216 , ALA A:229 , NAD A:3003 , HOH A:3337 , HOH A:3341	BINDING SITE FOR RESIDUE MLT A 3104
05	AC5	SOFTWARE	ARG C:92 , HOH C:3553	BINDING SITE FOR RESIDUE CL C 3201
06	AC6	SOFTWARE	ARG D:92 , HOH D:3318	BINDING SITE FOR RESIDUE CL D 3202
07	AC7	SOFTWARE	ARG A:92	BINDING SITE FOR RESIDUE CL A 3203
08	AC8	SOFTWARE	GLN C:263 , HOH C:3597	BINDING SITE FOR RESIDUE CL C 3204
09	AC9	SOFTWARE	ASN A:146	BINDING SITE FOR RESIDUE CL A 3205
10	BC1	SOFTWARE	VAL B:198 , PHE B:200 , HOH B:3533	BINDING SITE FOR RESIDUE CL B 3206
11	BC2	SOFTWARE	VAL D:198 , HOH D:3416	BINDING SITE FOR RESIDUE CL D 3207
12	BC3	SOFTWARE	SER B:15 , GLY B:16 , GLY B:17 , ILE B:18 , TYR B:38 , ASP B:39 , ILE B:40 , PRO B:81 , ALA B:82 , GLY B:83 , VAL B:84 , PRO B:85 , ASN B:99 , ILE B:102 , ILE B:122 , ASN B:124 , VAL B:151 , HIS B:182 , ALA B:229 , THR B:230 , MET B:233 , MLT B:3102 , HOH B:3404 , HOH B:3405 , HOH B:3415 , HOH B:3420 , HOH B:3429 , HOH B:3452 , HOH B:3476 , HOH B:3497 , HOH B:3501 , HOH B:3519 , HOH B:3527	BINDING SITE FOR RESIDUE NAD B 3001
13	BC4	SOFTWARE	GLY C:13 , SER C:15 , GLY C:16 , GLY C:17 , ILE C:18 , TYR C:38 , ASP C:39 , ILE C:40 , PRO C:81 , ALA C:82 , GLY C:83 , VAL C:84 , PRO C:85 , LEU C:95 , ASN C:99 , ILE C:102 , ILE C:122 , ASN C:124 , VAL C:126 , VAL C:151 , HIS C:182 , ALA C:229 , THR C:230 , MET C:233 , MLT C:3103 , HOH C:3509 , HOH C:3520 , HOH C:3526 , HOH C:3540 , HOH C:3557 , HOH C:3626 , HOH C:3636 , HOH C:3646 , HOH C:3691 , HOH C:3730	BINDING SITE FOR RESIDUE NAD C 3002
14	BC5	SOFTWARE	SER A:15 , GLY A:16 , GLY A:17 , ILE A:18 , TYR A:38 , ASP A:39 , ILE A:40 , PRO A:81 , ALA A:82 , GLY A:83 , VAL A:84 , PRO A:85 , ASN A:99 , ILE A:102 , ILE A:122 , ASN A:124 , VAL A:126 , VAL A:151 , HIS A:182 , ALA A:229 , THR A:230 , MET A:233 , MLT A:3104 , HOH A:3304 , HOH A:3305 , HOH A:3337 , HOH A:3344 , HOH A:3347 , HOH A:3379 , HOH A:3389 , HOH A:3427 , HOH A:3476 , HOH A:3478	BINDING SITE FOR RESIDUE NAD A 3003
15	BC6	SOFTWARE	SER D:15 , GLY D:16 , GLY D:17 , ILE D:18 , TYR D:38 , ASP D:39 , ILE D:40 , PRO D:81 , ALA D:82 , GLY D:83 , VAL D:84 , PRO D:85 , LEU D:95 , ASN D:99 , ILE D:102 , ILE D:122 , ASN D:124 , VAL D:126 , VAL D:151 , HIS D:182 , ALA D:229 , THR D:230 , MET D:233 , MLT D:3101 , HOH D:3220 , HOH D:3224 , HOH D:3236 , HOH D:3237 , HOH D:3251 , HOH D:3313 , HOH D:3335 , HOH D:3341 , HOH D:3361 , HOH D:3393 , HOH D:3399	BINDING SITE FOR RESIDUE NAD D 3004
16	BC7	SOFTWARE	ASN A:160 , PRO A:171 , ALA A:172 , VAL A:174 , ASN A:175 , ARG A:239 , ALA A:3302 , GLU B:54 , HOH B:3434	BINDING SITE FOR RESIDUE HIS A 3301
17	BC8	SOFTWARE	ARG A:239 , SER A:243 , HIS A:3301 , HOH A:3359	BINDING SITE FOR RESIDUE ALA A 3302
18	BC9	SOFTWARE	GLU A:54 , ASN B:160 , PRO B:171 , ALA B:172 , VAL B:174 , ASN B:175 , ARG B:239	BINDING SITE FOR RESIDUE HIS B 3401
19	CC1	SOFTWARE	ASN C:160 , PRO C:171 , ALA C:172 , VAL C:174 , ASN C:175 , ARG C:239 , GLU D:54	BINDING SITE FOR RESIDUE HIS C 3501

(no "SS Bond" information available for 2DFD)

Asymmetric Unit

No.	Residues
1	Asn A:124	-	Pro A:125
2	Thr A:195	-	Pro A:196
3	Asn B:124	-	Pro B:125
4	Thr B:195	-	Pro B:196
5	Asn C:124	-	Pro C:125
6	Thr C:195	-	Pro C:196
7	Asn D:124	-	Pro D:125
8	Thr D:195	-	Pro D:196

Asymmetric Unit (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_078001	G	37	R	MDHM_HUMAN	Disease (EIEE51)	782308462	A/B/C/D	G	19	R
2	UniProt	VAR_078002	P	133	L	MDHM_HUMAN	Disease (EIEE51)	375002796	A/B/C/D	P	115	L
3	UniProt	VAR_078003	P	207	L	MDHM_HUMAN	Disease (EIEE51)	---	A/B/C/D	P	189	L

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

Biological Unit 1 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_078001	G	37	R	MDHM_HUMAN	Disease (EIEE51)	782308462	A/B	G	19	R
2	UniProt	VAR_078002	P	133	L	MDHM_HUMAN	Disease (EIEE51)	375002796	A/B	P	115	L
3	UniProt	VAR_078003	P	207	L	MDHM_HUMAN	Disease (EIEE51)	---	A/B	P	189	L

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

Biological Unit 2 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_078001	G	37	R	MDHM_HUMAN	Disease (EIEE51)	782308462	C/D	G	19	R
2	UniProt	VAR_078002	P	133	L	MDHM_HUMAN	Disease (EIEE51)	375002796	C/D	P	115	L
3	UniProt	VAR_078003	P	207	L	MDHM_HUMAN	Disease (EIEE51)	---	C/D	P	189	L

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

Biological Unit 3 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_078001	G	37	R	MDHM_HUMAN	Disease (EIEE51)	782308462	A/B/C/D	G	19	R
2	UniProt	VAR_078002	P	133	L	MDHM_HUMAN	Disease (EIEE51)	375002796	A/B/C/D	P	115	L
3	UniProt	VAR_078003	P	207	L	MDHM_HUMAN	Disease (EIEE51)	---	A/B/C/D	P	189	L

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MDH	PS00068	Malate dehydrogenase active site signature.	MDHM_HUMAN	169-181	4	A:151-163 B:151-163 C:151-163 D:151-163

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MDH	PS00068	Malate dehydrogenase active site signature.	MDHM_HUMAN	169-181	2	A:151-163 B:151-163 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MDH	PS00068	Malate dehydrogenase active site signature.	MDHM_HUMAN	169-181	2	- - C:151-163 D:151-163

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MDH	PS00068	Malate dehydrogenase active site signature.	MDHM_HUMAN	169-181	4	A:151-163 B:151-163 C:151-163 D:151-163

Asymmetric Unit (8, 32)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000315758	1b	ENSE00001905498	chr7:75677385-75677544	160	MDHM_HUMAN	1-22	22	0	-	-
1.3b	ENST00000315758	3b	ENSE00000976862	chr7:75684148-75684316	169	MDHM_HUMAN	23-79	57	4	A:6-61 B:6-61 C:6-61 D:6-61	56 56 56 56
1.4c	ENST00000315758	4c	ENSE00001772678	chr7:75686728-75686811	84	MDHM_HUMAN	79-107	29	4	A:61-89 B:61-89 C:61-89 D:61-89	29 29 29 29
1.5a	ENST00000315758	5a	ENSE00001804254	chr7:75687287-75687396	110	MDHM_HUMAN	107-143	37	4	A:89-125 B:89-125 C:89-125 D:89-125	37 37 37 37
1.6b	ENST00000315758	6b	ENSE00001803022	chr7:75689691-75689816	126	MDHM_HUMAN	144-185	42	4	A:126-167 B:126-167 C:126-167 D:126-167	42 42 42 42
1.7	ENST00000315758	7	ENSE00001619723	chr7:75692833-75692910	78	MDHM_HUMAN	186-211	26	4	A:168-193 B:168-193 C:168-193 D:168-193	26 26 26 26
1.8	ENST00000315758	8	ENSE00001717303	chr7:75693657-75693756	100	MDHM_HUMAN	212-245	34	4	A:194-227 B:194-227 C:194-227 D:194-227	34 34 34 34
1.9a	ENST00000315758	9a	ENSE00001703408	chr7:75694120-75694271	152	MDHM_HUMAN	245-295	51	4	A:227-277 B:227-277 C:227-277 D:227-277	51 51 51 51
1.10c	ENST00000315758	10c	ENSE00001663150	chr7:75695597-75696826	1230	MDHM_HUMAN	296-338	43	4	A:278-319 B:278-319 C:278-319 D:278-319	42 42 42 42

Asymmetric 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:314
 aligned with MDHM_HUMAN | P40926 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:314
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    
           MDHM_HUMAN    24 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 337
               SCOP domains d2dfda1 A:6-150 automated matches                                                                                                                d2dfda2 A:151-319 automated matches                                                                                                                                       SCOP domains
               CATH domains 2dfdA01 A:6-151 NAD(P)-binding Rossmann-like Domain                                                                                               2dfdA02 A:152-318 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh.....eeeeee...hhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------R-----------------------------------------------------------------------------------------------L-------------------------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------MDH          ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:6-61 UniProt: 23-79 [INCOMPLETE]      ---------------------------Exon 1.5a  PDB: A:89-125             Exon 1.6b  PDB: A:126-167 UniProt: 144-185Exon 1.7  PDB: A:168-193  Exon 1.8  PDB: A:194-227          --------------------------------------------------Exon 1.10c  PDB: A:278-319 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.4c  PDB: A:61-89      -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.9a  PDB: A:227-277 UniProt: 245-295         ------------------------------------------ Transcript 1 (2)
                 2dfd A   6 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 319
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315

Chain B from PDB  Type:PROTEIN  Length:314
 aligned with MDHM_HUMAN | P40926 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:314
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    
           MDHM_HUMAN    24 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 337
               SCOP domains d2dfdb1 B:6-150 automated matches                                                                                                                d2dfdb2 B:151-319 automated matches                                                                                                                                       SCOP domains
               CATH domains 2dfdB01 B:6-151 NAD(P)-binding Rossmann-like Domain                                                                                               2dfdB02 B:152-318 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh.....eeeeee...hhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------R-----------------------------------------------------------------------------------------------L-------------------------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------MDH          ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: B:6-61 UniProt: 23-79 [INCOMPLETE]      ---------------------------Exon 1.5a  PDB: B:89-125             Exon 1.6b  PDB: B:126-167 UniProt: 144-185Exon 1.7  PDB: B:168-193  Exon 1.8  PDB: B:194-227          --------------------------------------------------Exon 1.10c  PDB: B:278-319 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.4c  PDB: B:61-89      -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.9a  PDB: B:227-277 UniProt: 245-295         ------------------------------------------ Transcript 1 (2)
                 2dfd B   6 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 319
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315

Chain C from PDB  Type:PROTEIN  Length:314
 aligned with MDHM_HUMAN | P40926 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:314
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    
           MDHM_HUMAN    24 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 337
               SCOP domains d2dfdc1 C:6-150 automated matches                                                                                                                d2dfdc2 C:151-319 automated matches                                                                                                                                       SCOP domains
               CATH domains 2dfdC01 C:6-151 NAD(P)-binding Rossmann-like Domain                                                                                               2dfdC02 C:152-318 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...eeeeeeee..hhhhhhhhhh......eeeeee...hhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------R-----------------------------------------------------------------------------------------------L-------------------------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------MDH          ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: C:6-61 UniProt: 23-79 [INCOMPLETE]      ---------------------------Exon 1.5a  PDB: C:89-125             Exon 1.6b  PDB: C:126-167 UniProt: 144-185Exon 1.7  PDB: C:168-193  Exon 1.8  PDB: C:194-227          --------------------------------------------------Exon 1.10c  PDB: C:278-319 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.4c  PDB: C:61-89      -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.9a  PDB: C:227-277 UniProt: 245-295         ------------------------------------------ Transcript 1 (2)
                 2dfd C   6 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 319
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315

Chain D from PDB  Type:PROTEIN  Length:314
 aligned with MDHM_HUMAN | P40926 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:314
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    
           MDHM_HUMAN    24 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 337
               SCOP domains d2dfdd1 D:6-150 automated matches                                                                                                                d2dfdd2 D:151-319 automated matches                                                                                                                                       SCOP domains
               CATH domains 2dfdD01 D:6-151 NAD(P)-binding Rossmann-like Domain                                                                                               2dfdD02 D:152-318 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhh......eeeeee...hhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------R-----------------------------------------------------------------------------------------------L-------------------------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------MDH          ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: D:6-61 UniProt: 23-79 [INCOMPLETE]      ---------------------------Exon 1.5a  PDB: D:89-125             Exon 1.6b  PDB: D:126-167 UniProt: 144-185Exon 1.7  PDB: D:168-193  Exon 1.8  PDB: D:194-227          --------------------------------------------------Exon 1.10c  PDB: D:278-319 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.4c  PDB: D:61-89      -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.9a  PDB: D:227-277 UniProt: 245-295         ------------------------------------------ Transcript 1 (2)
                 2dfd D   6 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 319
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: LDH C-terminal domain-like (172)

Superfamily: LDH C-terminal domain-like (172)

Family: Lactate & malate dehydrogenases, C-terminal domain (125)

Protein domain: automated matches (30)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2dfda2	A:151-319
1b	d2dfdb2	B:151-319
1c	d2dfdc2	C:151-319
1d	d2dfdd2	D:151-319

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: LDH N-terminal domain-like (117)

Protein domain: automated matches (15)

Human (Homo sapiens) [TaxId: 9606] (1)

2a	d2dfda1	A:6-150
2b	d2dfdb1	B:6-150
2c	d2dfdc1	C:6-150
2d	d2dfdd1	D:6-150

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

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

Human (Homo sapiens) (188)

1a	2dfdA01	A:6-151
1b	2dfdB01	B:6-151
1c	2dfdC01	C:6-151
1d	2dfdD01	D:6-151

Architecture: Alpha-Beta Complex (3881)

Topology: L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 (116)

Homologous Superfamily: L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2 (116)

Human (Homo sapiens) (4)

2a	2dfdA02	A:152-318
2b	2dfdB02	B:152-318
2c	2dfdC02	C:152-318
2d	2dfdD02	D:152-318

(no "Pfam Domain" information available for 2DFD)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MDHM_HUMAN | P40926)

molecular function
	GO:0030060	L-malate dehydrogenase activity	Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
	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:0046554	malate dehydrogenase (NADP+) activity	Catalysis of the reaction: (S)-malate + NADP+ = oxaloacetate + NADPH + H+.
	GO:0016615	malate dehydrogenase activity	Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
	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.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0043621	protein self-association	Interacting selectively and non-covalently with a domain within the same polypeptide.
biological process
	GO:0006734	NADH metabolic process	The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0006475	internal protein amino acid acetylation	The addition of an acetyl group to a non-terminal amino acid in a protein.
	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:0006107	oxaloacetate metabolic process	The chemical reactions and pathways involving oxaloacetate, the anion of oxobutanedioic acid, an important intermediate in metabolism, especially as a component of the TCA cycle.
	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:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	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.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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Access by PDB/NDB ID
	2dfd
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	MDHM_HUMAN \| P40926
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	1.1.1.37
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	MDHM_HUMAN \| P40926	:	4wle 4wlf 4wln 4wlo 4wlu 4wlv

1mld	REFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORCINE HEART AND THE CONSENSUS STRUCTURE FOR DICARBOXYLIC ACID OXIDOREDUCTASES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 12)

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Exons (8, 32)

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