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1WSV
Asym. Unit
Info
Asym.Unit (135 KB)
Biol.Unit 1 (131 KB)
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Title
:
CRYSTAL STRUCTURE OF HUMAN T-PROTEIN OF GLYCINE CLEAVAGE SYSTEM
Authors
:
K. Okamura-Ikeda, H. Hosaka, M. Yoshimura, E. Yamashita, S. Toma, A. Nakagawa, K. Fujiwara, Y. Motokawa, H. Taniguchi
Date
:
11 Nov 04 (Deposition) - 16 Aug 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Glycine-Cleavage Sytem, Aminomethyl Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Okamura-Ikeda, H. Hosaka, M. Yoshimura, E. Yamashita, S. Toma, A. Nakagawa, K. Fujiwara, Y. Motokawa, H. Taniguchi
Crystal Structure Of Human T-Protein Of Glycine Cleavage System At 2. 0A Resolution And Its Implication For Understanding Non-Ketotic Hyperglycinemia
J. Mol. Biol. V. 351 1146 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 13)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
1i: SULFATE ION (SO4i)
1j: SULFATE ION (SO4j)
1k: SULFATE ION (SO4k)
2a: N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-M... (THHa)
2b: N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-M... (THHb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
11
Ligand/Ion
SULFATE ION
2
THH
2
Ligand/Ion
N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID
[
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]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:214 , HOH A:3167 , HOH A:3168 , ASP B:12 , VAL B:213 , HOH B:4011
BINDING SITE FOR RESIDUE SO4 A 2001
02
AC2
SOFTWARE
ARG A:172 , HOH A:3201 , ARG B:290 , GLY B:317 , THR B:318 , TYR B:336
BINDING SITE FOR RESIDUE SO4 A 2002
03
AC3
SOFTWARE
HIS A:37 , ARG A:303 , HOH A:3137 , HOH A:3278 , HOH A:3370
BINDING SITE FOR RESIDUE SO4 A 2003
04
AC4
SOFTWARE
ARG A:303 , ARG A:353 , HOH A:3250 , HOH A:3270
BINDING SITE FOR RESIDUE SO4 A 2004
05
AC5
SOFTWARE
HIS A:43 , LYS A:226 , LYS A:278
BINDING SITE FOR RESIDUE SO4 A 2005
06
AC6
SOFTWARE
ARG A:287 , HOH A:3244
BINDING SITE FOR RESIDUE SO4 A 2006
07
AC7
SOFTWARE
SER B:259 , LEU B:260 , SER B:261 , TRP B:262 , ARG B:291 , HOH B:4094
BINDING SITE FOR RESIDUE SO4 B 2007
08
AC8
SOFTWARE
SER A:259 , LEU A:260 , SER A:261 , TRP A:262 , ARG A:291 , HOH A:3055 , HOH A:3252 , HOH A:3336
BINDING SITE FOR RESIDUE SO4 A 2008
09
AC9
SOFTWARE
ARG B:303 , ARG B:353 , HOH B:4029
BINDING SITE FOR RESIDUE SO4 B 2009
10
BC1
SOFTWARE
HIS B:37 , ARG B:303 , PRO B:324 , HOH B:4004 , HOH B:4106
BINDING SITE FOR RESIDUE SO4 B 2010
11
BC2
SOFTWARE
HIS A:17 , ARG A:34 , ARG B:7 , HOH B:4160
BINDING SITE FOR RESIDUE SO4 A 2011
12
BC3
SOFTWARE
MET A:56 , LEU A:88 , ASP A:101 , LEU A:102 , ILE A:103 , VAL A:115 , ASN A:117 , PHE A:176 , MET A:177 , GLY A:196 , TYR A:197 , GLU A:204 , ARG A:233 , LEU A:242 , TRP A:262 , TYR A:371 , HOH A:3016 , HOH A:3025 , HOH A:3027 , HOH A:3198 , HOH A:3235
BINDING SITE FOR RESIDUE THH A 3001
13
BC4
SOFTWARE
MET B:56 , THR B:87 , LEU B:88 , ASP B:101 , ILE B:103 , VAL B:115 , ASN B:117 , PHE B:176 , MET B:177 , GLY B:196 , TYR B:197 , GLU B:204 , ARG B:233 , TRP B:262 , TYR B:371 , HOH B:4012 , HOH B:4050 , HOH B:4085 , HOH B:4099 , HOH B:4110 , HOH B:4193
BINDING SITE FOR RESIDUE THH B 4001
[
close Site info
]
SAPs(SNPs)/Variants
(7, 14)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_007951 (H14R, chain A/B, )
2: VAR_007952 (G19R, chain A/B, )
3: VAR_016847 (N117I, chain A/B, )
4: VAR_016848 (E183K, chain A/B, )
5: VAR_007953 (G241D, chain A/B, )
6: VAR_007954 (D248H, chain A/B, )
7: VAR_007955 (R292H, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_007951
H
42
R
GCST_HUMAN
Disease (NKH)
---
A/B
H
14
R
2
UniProt
VAR_007952
G
47
R
GCST_HUMAN
Disease (NKH)
---
A/B
G
19
R
3
UniProt
VAR_016847
N
145
I
GCST_HUMAN
Disease (NKH)
---
A/B
N
117
I
4
UniProt
VAR_016848
E
211
K
GCST_HUMAN
Disease (NKH)
116192290
A/B
E
183
K
5
UniProt
VAR_007953
G
269
D
GCST_HUMAN
Disease (NKH)
---
A/B
G
241
D
6
UniProt
VAR_007954
D
276
H
GCST_HUMAN
Disease (NKH)
---
A/B
D
248
H
7
UniProt
VAR_007955
R
320
H
GCST_HUMAN
Disease (NKH)
---
A/B
R
292
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(8, 16)
Info
All Exons
Exon 1.1m (A:4-58 | B:4-58)
Exon 1.1s (A:59-85 | B:59-85)
Exon 1.2c (A:86-129 | B:86-129)
Exon 1.2k (A:130-156 | B:130-156)
Exon 1.2o (A:156-204 | B:156-204)
Exon 1.2s (A:205-265 | B:205-265)
Exon 1.4b (A:265-317 | B:265-317)
Exon 1.5e (A:317-374 | B:317-374)
View:
Select:
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All Exon Boundaries
1: Boundary 1.1a/1.1m
2: Boundary 1.1m/1.1s
3: Boundary 1.1s/1.2c
4: Boundary 1.2c/1.2k
5: Boundary 1.2k/1.2o
6: Boundary 1.2o/1.2s
7: Boundary 1.2s/1.4b
8: Boundary 1.4b/1.5e
9: Boundary 1.5e/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000273588
1a
ENSE00001875220
chr3:
49460186-49459794
393
GCST_HUMAN
1-30
30
0
-
-
1.1m
ENST00000273588
1m
ENSE00001616814
chr3:
49459704-49459537
168
GCST_HUMAN
31-86
56
2
A:4-58
B:4-58
55
55
1.1s
ENST00000273588
1s
ENSE00001754606
chr3:
49459005-49458925
81
GCST_HUMAN
87-113
27
2
A:59-85
B:59-85
27
27
1.2c
ENST00000273588
2c
ENSE00001608529
chr3:
49457775-49457644
132
GCST_HUMAN
114-157
44
2
A:86-129
B:86-129
44
44
1.2k
ENST00000273588
2k
ENSE00001775658
chr3:
49457221-49457143
79
GCST_HUMAN
158-184
27
2
A:130-156
B:130-156
27
27
1.2o
ENST00000273588
2o
ENSE00001674578
chr3:
49456838-49456693
146
GCST_HUMAN
184-232
49
2
A:156-204
B:156-204
49
49
1.2s
ENST00000273588
2s
ENSE00001676172
chr3:
49456584-49456404
181
GCST_HUMAN
233-293
61
2
A:205-265
B:205-265
61
61
1.4b
ENST00000273588
4b
ENSE00001794841
chr3:
49455406-49455251
156
GCST_HUMAN
293-345
53
2
A:265-317
B:265-317
53
53
1.5e
ENST00000273588
5e
ENSE00000968358
chr3:
49455151-49454212
940
GCST_HUMAN
345-403
59
2
A:317-374
B:317-374
58
58
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1wsvA01 (A:4-55,A:147-240)
1b: CATH_1wsvB01 (B:4-55,B:147-240)
2a: CATH_1wsvA04 (A:287-363)
2b: CATH_1wsvB04 (B:287-363)
View:
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Classes
(
)
(
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Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
Probable tRNA modification gtpase trme; domain 1
(18)
Human (Homo sapiens)
(2)
1a
1wsvA01
A:4-55,A:147-240
1b
1wsvB01
B:4-55,B:147-240
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
Aminomethyltransferase beta-barrel domains
(17)
Human (Homo sapiens)
(2)
2a
1wsvA04
A:287-363
2b
1wsvB04
B:287-363
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_GCV_T_1wsvB01 (B:50-263)
1b: PFAM_GCV_T_1wsvB02 (B:50-263)
2a: PFAM_GCV_T_C_1wsvB03 (B:272-364)
2b: PFAM_GCV_T_C_1wsvB04 (B:272-364)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FBD
(14)
Family
:
GCV_T
(12)
Homo sapiens (Human)
(2)
1a
GCV_T-1wsvB01
B:50-263
1b
GCV_T-1wsvB02
B:50-263
Clan
:
no clan defined [family: GCV_T_C]
(10)
Family
:
GCV_T_C
(10)
Homo sapiens (Human)
(2)
2a
GCV_T_C-1wsvB03
B:272-364
2b
GCV_T_C-1wsvB04
B:272-364
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