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1WSR
Biol. Unit 2
Info
Asym.Unit (142 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (138 KB)
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(1)
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
:
10 Nov 04 (Deposition) - 16 Aug 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: 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
(1, 8)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
8
Ligand/Ion
SULFATE ION
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:137 , HIS A:214 , HOH A:2482 , ASP B:12 , VAL B:213 , HOH B:2031 , HOH B:2172
BINDING SITE FOR RESIDUE SO4 A 2001
02
AC2
SOFTWARE
ARG A:172 , HOH A:2392 , ARG B:290 , GLY B:317 , THR B:318 , HOH B:2110 , HOH B:2484
BINDING SITE FOR RESIDUE SO4 A 2002
03
AC3
SOFTWARE
HIS A:37 , ARG A:303 , PRO A:324 , HOH A:2330 , HOH A:2494 , HOH A:2524
BINDING SITE FOR RESIDUE SO4 A 2003
04
AC4
SOFTWARE
ARG A:303 , ARG A:353
BINDING SITE FOR RESIDUE SO4 A 2004
05
AC5
SOFTWARE
HIS A:43 , LYS A:226 , LYS A:278 , HOH A:2172 , HOH A:2296 , HOH A:2453
BINDING SITE FOR RESIDUE SO4 A 2005
06
AC6
SOFTWARE
ARG A:287
BINDING SITE FOR RESIDUE SO4 A 2006
07
AC7
SOFTWARE
SER B:259 , LEU B:260 , SER B:261 , TRP B:262 , HOH B:2488
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:2156 , HOH A:2515 , HOH A:2575
BINDING SITE FOR RESIDUE SO4 A 2008
09
AC9
SOFTWARE
ARG B:303 , ARG B:353
BINDING SITE FOR RESIDUE SO4 B 2009
10
BC1
SOFTWARE
HIS B:37 , ARG B:303 , PRO B:324 , HOH B:2315 , HOH B:2544
BINDING SITE FOR RESIDUE SO4 B 2010
11
BC2
SOFTWARE
HIS A:17 , ARG A:34 , ARG B:7 , HOH B:2138 , HOH B:2179 , HOH B:2321 , HOH B:2378 , HOH B:2454
BINDING SITE FOR RESIDUE SO4 A 2011
[
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]
SAPs(SNPs)/Variants
(7, 14)
Info
(mutated residues are only available for the asymmetric unit)
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)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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_1wsrA01 (A:4-55,A:147-240)
1b: CATH_1wsrB01 (B:4-55,B:147-240)
2a: CATH_1wsrA04 (A:287-363)
2b: CATH_1wsrB04 (B:287-363)
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)
(
)
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
1wsrA01
A:4-55,A:147-240
1b
1wsrB01
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
1wsrA04
A:287-363
2b
1wsrB04
B:287-363
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_GCV_T_1wsrB01 (B:50-263)
1b: PFAM_GCV_T_1wsrB02 (B:50-263)
2a: PFAM_GCV_T_C_1wsrB03 (B:272-364)
2b: PFAM_GCV_T_C_1wsrB04 (B:272-364)
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Clans
(
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(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
FBD
(14)
Family
:
GCV_T
(12)
Homo sapiens (Human)
(2)
1a
GCV_T-1wsrB01
B:50-263
1b
GCV_T-1wsrB02
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-1wsrB03
B:272-364
2b
GCV_T_C-1wsrB04
B:272-364
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Asym.Unit (142 KB)
Header - Asym.Unit
Biol.Unit 1 (138 KB)
Header - Biol.Unit 1
Biol.Unit 2 (138 KB)
Header - Biol.Unit 2
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