2YDX - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

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 S-ADENOSYLMETHIONINE SYNTHETASE 2, BETA SUBUNIT

Authors :   J. R. C. Muniz, N. Shafqat, A. C. W. Pike, W. W. Yue, M. Vollmar, V. Papagri A. Roos, O. Gileadi, F. Von Delft, K. L. Kavanagh, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, U. Oppermann

Date :   25 Mar 11 (Deposition) - 27 Apr 11 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Oxidoreductase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Shafqat, J. R. C. Muniz, E. S. Pilka, E. Papagrigoriou, F. Von Delft U. Oppermann, W. W. Yue
Insight Into S-Adenosylmethionine Biosynthesis From The Crystal Structures Of The Human Methionine Adenosyltransferase Catalytic And Regulatory Subunits.
Biochem. J. V. 452 27 2013
PubMed-ID: 23425511 | Reference-DOI: 10.1042/BJ20121580

Molecule 1 - METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Expression System Vector	:	PNIC-CTHF
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 28-335
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DTDP-4-KETO-6-DEOXY-D-GLUCOSE 4-REDUCTASE, METHIONINE ADENOSYLTRANSFERASE II BETA, MAT II BETA, S-ADENOSYLMETHIONINE SYNTHETASE 2, MAT2B

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:		B
Biological Unit 2 (1x)	:	A		C
Biological Unit 3 (1x)	:				D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 35)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	SO4	19	Ligand/Ion	SULFATE ION
4	STL	10	Ligand/Ion	RESVERATROL
5	TXP	1	Ligand/Ion	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	SO4	10	Ligand/Ion	SULFATE ION
4	STL	4	Ligand/Ion	RESVERATROL
5	TXP	-1	Ligand/Ion	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDEPHOSPHATE

Biological Unit 2 (3, 13)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	SO4	7	Ligand/Ion	SULFATE ION
4	STL	4	Ligand/Ion	RESVERATROL
5	TXP	-1	Ligand/Ion	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDEPHOSPHATE

Biological Unit 3 (4, 13)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	SO4	7	Ligand/Ion	SULFATE ION
4	STL	4	Ligand/Ion	RESVERATROL
5	TXP	1	Ligand/Ion	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (35, 35)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:328 , ARG A:329 , THR A:331 , VAL A:332 , HIS A:334 , GLU A:336 , ASN A:337 , GLU C:68 , ASN C:76 , ALA C:77 , HIS C:80 , ASP C:84	BINDING SITE FOR RESIDUE STL A 501
02	AC2	SOFTWARE	ARG A:97 , SER A:136 , ASP A:137 , TYR A:138 , TYR A:159 , ILE A:184 , GLU A:193 , SER A:195 , ALA A:196 , ARG A:219 , NAP A:1339	BINDING SITE FOR RESIDUE STL A 502
03	AC3	SOFTWARE	SER B:136 , ASP B:137 , TYR B:159 , ILE B:184 , GLU B:193 , SER B:195 , ALA B:196 , ARG B:219 , NAP B:1339 , SO4 B:1342	BINDING SITE FOR RESIDUE STL B 501
04	AC4	SOFTWARE	GLU B:68 , ASN B:76 , ALA B:77 , HIS B:80 , ASP B:84 , TRP B:328 , ARG B:329 , THR B:331 , VAL B:332 , HIS B:334 , GLU B:336 , ASN B:337	BINDING SITE FOR RESIDUE STL B 502
05	AC5	SOFTWARE	GLU A:68 , ASN A:76 , HIS A:80 , ASP A:84 , TRP C:328 , ARG C:329 , THR C:331 , HIS C:334 , GLU C:336 , ASN C:337 , HOH C:2095	BINDING SITE FOR RESIDUE STL C 501
06	AC6	SOFTWARE	ARG C:97 , SER C:136 , ASP C:137 , TYR C:159 , ILE C:184 , GLU C:193 , SER C:195 , ALA C:196 , ARG C:219 , NAP C:1339 , SO4 C:1340	BINDING SITE FOR RESIDUE STL C 502
07	AC7	SOFTWARE	ARG D:97 , SER D:136 , ASP D:137 , TYR D:159 , ILE D:184 , GLU D:193 , SER D:195 , ALA D:196 , ARG D:219 , NAP D:1339 , SO4 D:1341	BINDING SITE FOR RESIDUE STL D 501
08	AC8	SOFTWARE	TRP D:328 , ARG D:329 , THR D:331 , VAL D:332 , HIS D:334 , GLU D:336 , ASN D:337 , GLU E:68 , ASP E:74 , ASN E:76 , ALA E:77 , HIS E:80 , ASP E:84	BINDING SITE FOR RESIDUE STL D 502
09	AC9	SOFTWARE	ARG E:97 , ARG E:98 , SER E:136 , ASP E:137 , TYR E:159 , ILE E:184 , GLU E:193 , ALA E:196 , ARG E:219 , TXP E:1339	BINDING SITE FOR RESIDUE STL E 501
10	BC1	SOFTWARE	GLU D:68 , ASP D:74 , ASN D:76 , ALA D:77 , HIS D:80 , ASP D:84 , TRP E:328 , ARG E:329 , THR E:331 , HIS E:334 , GLU E:336 , ASN E:337	BINDING SITE FOR RESIDUE STL E 502
11	BC2	SOFTWARE	GLY A:35 , THR A:37 , GLY A:38 , LEU A:39 , LEU A:40 , PHE A:60 , ARG A:61 , ARG A:62 , VAL A:70 , ASN A:71 , LEU A:72 , CYS A:93 , ALA A:94 , ALA A:95 , ARG A:97 , LEU A:112 , ILE A:134 , SER A:135 , TYR A:159 , LYS A:163 , ILE A:182 , PRO A:183 , ILE A:184 , LEU A:185 , STL A:502 , HOH A:2006 , HOH A:2025 , HOH A:2071 , HOH A:2148 , HOH A:2149 , HOH A:2150 , HOH A:2151 , HOH A:2152	BINDING SITE FOR RESIDUE NAP A1339
12	BC3	SOFTWARE	GLY D:35 , THR D:37 , GLY D:38 , LEU D:39 , LEU D:40 , PHE D:60 , ARG D:61 , ARG D:62 , VAL D:70 , ASN D:71 , LEU D:72 , CYS D:93 , ALA D:94 , ALA D:95 , ARG D:97 , LEU D:112 , ILE D:134 , SER D:135 , TYR D:159 , LYS D:163 , ILE D:182 , PRO D:183 , LEU D:185 , STL D:501 , HOH D:2004 , HOH D:2017 , HOH D:2063 , HOH D:2064	BINDING SITE FOR RESIDUE NAP D1339
13	BC4	SOFTWARE	GLY C:35 , THR C:37 , GLY C:38 , LEU C:39 , LEU C:40 , PHE C:60 , ARG C:61 , ARG C:62 , VAL C:70 , ASN C:71 , LEU C:72 , CYS C:93 , ALA C:94 , ALA C:95 , ARG C:97 , LEU C:112 , ILE C:134 , SER C:135 , TYR C:159 , LYS C:163 , ILE C:182 , PRO C:183 , ILE C:184 , LEU C:185 , STL C:502 , HOH C:2047 , HOH C:2096 , HOH C:2097 , HOH C:2098 , HOH C:2099 , HOH C:2100 , HOH C:2101	BINDING SITE FOR RESIDUE NAP C1339
14	BC5	SOFTWARE	GLY E:35 , THR E:37 , GLY E:38 , LEU E:39 , LEU E:40 , PHE E:60 , ARG E:61 , ARG E:62 , VAL E:70 , ASN E:71 , LEU E:72 , CYS E:93 , ALA E:94 , ALA E:95 , ARG E:97 , LEU E:112 , ILE E:134 , SER E:135 , TYR E:159 , LYS E:163 , ILE E:182 , PRO E:183 , LEU E:185 , STL E:501 , HOH E:2003 , HOH E:2064	BINDING SITE FOR RESIDUE TXP E1339
15	BC6	SOFTWARE	GLY B:35 , THR B:37 , GLY B:38 , LEU B:39 , LEU B:40 , PHE B:60 , ARG B:61 , ARG B:62 , VAL B:70 , ASN B:71 , LEU B:72 , CYS B:93 , ALA B:94 , ALA B:95 , ARG B:97 , LEU B:112 , ILE B:134 , SER B:135 , TYR B:159 , LYS B:163 , ILE B:182 , PRO B:183 , LEU B:185 , STL B:501 , HOH B:2004 , HOH B:2005 , HOH B:2039 , HOH B:2067 , HOH B:2122 , HOH B:2125 , HOH B:2126 , HOH B:2127	BINDING SITE FOR RESIDUE NAP B1339
16	BC7	SOFTWARE	ARG C:30 , HIS C:88 , ARG E:30 , HIS E:88	BINDING SITE FOR RESIDUE SO4 E1340
17	BC8	SOFTWARE	ARG A:30 , HIS A:88 , HOH A:2153 , HOH A:2154 , ARG D:30 , HIS D:88	BINDING SITE FOR RESIDUE SO4 A1340
18	BC9	SOFTWARE	ARG B:30 , HIS B:88	BINDING SITE FOR RESIDUE SO4 B1340
19	CC1	SOFTWARE	TYR C:138 , ARG C:219 , ARG C:289 , STL C:502 , HOH C:2102 , HOH C:2103	BINDING SITE FOR RESIDUE SO4 C1340
20	CC2	SOFTWARE	GLN E:218 , GLN E:255 , ARG E:291 , ASN E:292	BINDING SITE FOR RESIDUE SO4 E1341
21	CC3	SOFTWARE	GLN C:218 , GLN C:255 , ARG C:291 , ASN C:292	BINDING SITE FOR RESIDUE SO4 C1341
22	CC4	SOFTWARE	GLN B:218 , GLN B:255 , ARG B:291 , ASN B:292	BINDING SITE FOR RESIDUE SO4 B1341
23	CC5	SOFTWARE	GLN D:218 , GLN D:255 , ARG D:291 , ASN D:292	BINDING SITE FOR RESIDUE SO4 D1340
24	CC6	SOFTWARE	TYR B:138 , ALA B:196 , ARG B:219 , LYS B:258 , ARG B:289 , STL B:501	BINDING SITE FOR RESIDUE SO4 B1342
25	CC7	SOFTWARE	ARG A:327 , TRP A:328 , ARG A:329 , HIS C:54 , VAL C:56	BINDING SITE FOR RESIDUE SO4 A1341
26	CC8	SOFTWARE	TYR D:138 , ALA D:196 , ARG D:219 , LYS D:258 , ARG D:289 , STL D:501	BINDING SITE FOR RESIDUE SO4 D1341
27	CC9	SOFTWARE	PHE B:220 , SER B:251 , GLY B:252 , ASN B:253 , GLN B:294 , LEU B:295 , ARG B:308	BINDING SITE FOR RESIDUE SO4 B1343
28	DC1	SOFTWARE	SER A:251 , GLY A:252 , ASN A:253 , GLN A:294 , LEU A:295 , ARG A:308 , HOH A:2155	BINDING SITE FOR RESIDUE SO4 A1342
29	DC2	SOFTWARE	HIS B:54 , ARG B:327 , TRP B:328 , ARG B:329	BINDING SITE FOR RESIDUE SO4 B1344
30	DC3	SOFTWARE	HIS A:54 , VAL A:56 , ARG C:327 , TRP C:328 , ARG C:329	BINDING SITE FOR RESIDUE SO4 C1342
31	DC4	SOFTWARE	ARG D:327 , TRP D:328 , ARG D:329 , HIS E:54 , VAL E:56 , HOH E:2017	BINDING SITE FOR RESIDUE SO4 D1342
32	DC5	SOFTWARE	HIS D:54 , VAL D:56 , ARG E:327 , TRP E:328 , ARG E:329	BINDING SITE FOR RESIDUE SO4 E1342
33	DC6	SOFTWARE	TYR E:138 , ARG E:219 , LYS E:258 , ARG E:289	BINDING SITE FOR RESIDUE SO4 E1343
34	DC7	SOFTWARE	TYR A:138 , HOH A:2156	BINDING SITE FOR RESIDUE SO4 A1343
35	DC8	SOFTWARE	ASP A:137 , PRO A:183 , PHE A:220 , HOH A:2086 , HOH A:2098 , HOH A:2125	BINDING SITE FOR RESIDUE CA A1344

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

Asymmetric Unit

No.	Residues
1	Arg A:64	-	Pro A:65
2	Pro A:145	-	Pro A:146
3	Arg B:64	-	Pro B:65
4	Pro B:145	-	Pro B:146
5	Arg C:64	-	Pro C:65
6	Pro C:145	-	Pro C:146
7	Arg D:64	-	Pro D:65
8	Pro D:145	-	Pro D:146
9	Arg E:64	-	Pro E:65
10	Pro E:145	-	Pro E:146

Asymmetric Unit (1, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032318	A	293	T	MAT2B_HUMAN	Polymorphism	17849948	A/B/C/D/E	A	293	T

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032318	A	293	T	MAT2B_HUMAN	Polymorphism	17849948	B	A	293	T

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

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032318	A	293	T	MAT2B_HUMAN	Polymorphism	17849948	A/C	A	293	T

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

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032318	A	293	T	MAT2B_HUMAN	Polymorphism	17849948	D/E	A	293	T

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

(no "PROSITE Motif" information available for 2YDX)

(no "Exon" information available for 2YDX)

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:312
 aligned with MAT2B_HUMAN | Q9NZL9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:312
                                                                                                                                                                                                                                                                                                                                             334    
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       | -  
          MAT2B_HUMAN    27 PNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFH----   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee........ee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh................hhhhhhhhhhhhhhhhhh...eeeee..ee....hhhhh.hhhhhhhhhh....eeee.......eehhhhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhh.....eeee..hhhhhhh........hhhhhhh......hhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ydx A  27 MNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFHAENL 338
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with MAT2B_HUMAN | Q9NZL9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:312
                                                                                                                                                                                                                                                                                                                                             334    
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       | -  
          MAT2B_HUMAN    27 PNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFH----   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee........ee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh................hhhhhhhhhhhhhhhhhh...eeeee..ee....hhhhh.hhhhhhhhhh....eeee.......eehhhhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhh.....eeee.....hhhhh.......hhhhhh.......hhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ydx B  27 MNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFHAENL 338
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336

Chain C from PDB  Type:PROTEIN  Length:312
 aligned with MAT2B_HUMAN | Q9NZL9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:312
                                                                                                                                                                                                                                                                                                                                             334    
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       | -  
          MAT2B_HUMAN    27 PNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFH----   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee........ee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh................hhhhhhhhhhhhhhhhhh...eeeee..ee....hhhhh.hhhhhhhhhh....eeee.......eehhhhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhh.....eeee.....hhhhh.......hhhhhhh......hhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ydx C  27 MNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFHAENL 338
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336

Chain D from PDB  Type:PROTEIN  Length:312
 aligned with MAT2B_HUMAN | Q9NZL9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:312
                                                                                                                                                                                                                                                                                                                                             334    
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       | -  
          MAT2B_HUMAN    27 PNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFH----   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee........ee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh................hhhhhhhhhhhhhhhhhh...eeeee..ee....hhhhh.hhhhhhhhhh....eeee.......eehhhhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhh.....eeee.....hhhhh.......hhhhhhh......hhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ydx D  27 MNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFHAENL 338
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336

Chain E from PDB  Type:PROTEIN  Length:312
 aligned with MAT2B_HUMAN | Q9NZL9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:312
                                                                                                                                                                                                                                                                                                                                             334    
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       | -  
          MAT2B_HUMAN    27 PNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFH----   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --RmlD_sub_bind-2ydxE01 E:29-324                                                                                                                                                                                                                                                                          -------------- Pfam domains (1)
           Pfam domains (2) --RmlD_sub_bind-2ydxE02 E:29-324                                                                                                                                                                                                                                                                          -------------- Pfam domains (2)
           Pfam domains (3) --RmlD_sub_bind-2ydxE03 E:29-324                                                                                                                                                                                                                                                                          -------------- Pfam domains (3)
           Pfam domains (4) --RmlD_sub_bind-2ydxE04 E:29-324                                                                                                                                                                                                                                                                          -------------- Pfam domains (4)
           Pfam domains (5) --RmlD_sub_bind-2ydxE05 E:29-324                                                                                                                                                                                                                                                                          -------------- Pfam domains (5)
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee........ee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh................hhhhhhhhhhhhhhhhhh...eeeee..ee....hhhhh.hhhhhhhhhh....eeee.......eehhhhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhh.....eeee.....hhhhh.......hhhhhhh......hhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ydx E  27 MNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLIDKRWRQTVFHAENL 338
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336

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 '\|'

(no "SCOP Domain" information available for 2YDX)

(no "CATH Domain" information available for 2YDX)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: RmlD_sub_bind (7)

Homo sapiens (Human) (2)

1a	RmlD_sub_bind-2ydxE01	E:29-324
1b	RmlD_sub_bind-2ydxE02	E:29-324
1c	RmlD_sub_bind-2ydxE03	E:29-324
1d	RmlD_sub_bind-2ydxE04	E:29-324
1e	RmlD_sub_bind-2ydxE05	E:29-324

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (MAT2B_HUMAN | Q9NZL9)

molecular function
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0048270	methionine adenosyltransferase regulator activity	Modulates the activity of methionine adenosyltransferase.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006556	S-adenosylmethionine biosynthetic process	The chemical reactions and pathways resulting in the formation of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0048269	methionine adenosyltransferase complex	A multimeric enzyme complex composed of variable numbers of catalytic alpha subunits, and noncatalytic beta subunits. The beta subunits are believed to have a regulatory function. The enzyme complex catalyzes the synthesis of S-adenosylmethionine (AdoMet), which is the major methyl group donor, participating in the methylation of proteins, DNA, RNA, phospholipids, and other small molecules.
	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: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.

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	2ydx
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	MAT2B_HUMAN \| Q9NZL9	:	2ydy 4ktt 4ktv 4ndn

2ydy	CRYSTAL STRUCTURE OF HUMAN S-ADENOSYLMETHIONINE SYNTHETASE 2, BETA SUBUNIT IN ORTHORHOMBIC CRYSTAL FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 35)

Sites (35, 35)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 5)

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Exons (0, 0)

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