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2YDX
Asym. Unit
Info
Asym.Unit (446 KB)
Biol.Unit 1 (221 KB)
Biol.Unit 2 (167 KB)
Biol.Unit 3 (163 KB)
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(1)
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
[
close entry info
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Hetero Components
(5, 35)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
2d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
4a: RESVERATROL (STLa)
4b: RESVERATROL (STLb)
4c: RESVERATROL (STLc)
4d: RESVERATROL (STLd)
4e: RESVERATROL (STLe)
4f: RESVERATROL (STLf)
4g: RESVERATROL (STLg)
4h: RESVERATROL (STLh)
4i: RESVERATROL (STLi)
4j: RESVERATROL (STLj)
5a: 1,4,5,6-TETRAHYDRONICOTINAMIDE ADE... (TXPa)
View:
Select:
Label:
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
[
close Hetero Component info
]
Sites
(35, 35)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
View:
Select:
Label:
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
[
close Site info
]
SAPs(SNPs)/Variants
(1, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_032318 (A293T, chain A/B/C/D/E, )
View:
Select:
Label:
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)
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_RmlD_sub_bind_2ydxE01 (E:29-324)
1b: PFAM_RmlD_sub_bind_2ydxE02 (E:29-324)
1c: PFAM_RmlD_sub_bind_2ydxE03 (E:29-324)
1d: PFAM_RmlD_sub_bind_2ydxE04 (E:29-324)
1e: PFAM_RmlD_sub_bind_2ydxE05 (E:29-324)
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Organisms
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)
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
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