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Getting 'Biological Unit' information from database.
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3H9E
Biol. Unit 1
Info
Asym.Unit (129 KB)
Biol.Unit 1 (239 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN SPERM-SPECIFIC GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPDS) COMPLEX WITH NAD AND PHOSPHATE
Authors
:
A. Chaikuad, N. Shafqat, W. Yue, R. Cocking, J. E. Bray, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, U. Oppermann, Structural Genomics Consortium (Sgc)
Date
:
30 Apr 09 (Deposition) - 26 May 09 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.72
Chains
:
Asym. Unit : O,P
Biol. Unit 1: O,P (2x)
Keywords
:
Oxidoreductase, Structural Genomics, Structural Genomics Consortium, Sgc, Glycolysis, Nad, Phosphoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Chaikuad, N. Shafqat, R. Al-Mokhtar, G. Cameron, A. R. Clarke, R. L. Brady, U. Oppermann, J. Frayne, W. W. Yue
Structure And Kinetic Characterization Of Human Sperm-Specific Glyceraldehyde-3-Phosphate Dehydrogenase, Gapds.
Biochem. J. V. 435 401 2011
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Hetero Components
(3, 40)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
28
Ligand/Ion
1,2-ETHANEDIOL
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
PO4
8
Ligand/Ion
PHOSPHATE ION
[
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Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH O:27 , HOH O:32 , HOH O:56 , ASN O:81 , GLY O:82 , PHE O:83 , GLY O:84 , ARG O:85 , ILE O:86 , ASP O:106 , PRO O:107 , PHE O:108 , LYS O:151 , SER O:169 , THR O:170 , GLY O:171 , TYR O:173 , SER O:193 , ALA O:194 , ALA O:255 , ASN O:388 , TYR O:392 , PO4 O:415 , HOH O:424 , HOH O:439 , HOH O:448 , HOH O:456 , HOH O:459 , HOH O:465 , HOH O:472 , HOH O:559 , HOH O:563 , HOH O:569 , HOH O:571 , HOH O:579 , HOH O:602
BINDING SITE FOR RESIDUE NAD O 2
02
AC2
SOFTWARE
NAD O:2 , THR O:254 , THR O:256 , ARG O:306 , HOH O:424 , HOH O:455 , HOH O:468 , HOH O:492 , HOH O:532 , HOH O:559 , HOH O:595
BINDING SITE FOR RESIDUE PO4 O 415
03
AC3
SOFTWARE
HOH O:37 , SER O:223 , CYS O:224 , THR O:225 , HIS O:251 , THR O:283 , GLY O:284 , HOH O:424 , HOH O:455 , HOH O:564 , HOH O:595
BINDING SITE FOR RESIDUE PO4 O 4
04
AC4
SOFTWARE
ALA O:267 , TRP O:268 , HOH O:527
BINDING SITE FOR RESIDUE EDO O 8
05
AC5
SOFTWARE
PRO O:200 , MET O:201 , ASN O:207 , LYS O:291 , HOH O:577
BINDING SITE FOR RESIDUE EDO O 9
06
AC6
SOFTWARE
GLU O:244 , ARG O:320 , HOH O:600 , ARG P:320 , ASN P:376 , ASN P:378 , HOH P:618
BINDING SITE FOR RESIDUE EDO O 14
07
AC7
SOFTWARE
GLY O:205 , ASN O:207 , GLU O:208 , ASN O:209 , HOH O:567
BINDING SITE FOR RESIDUE EDO O 15
08
AC8
SOFTWARE
LYS O:331
BINDING SITE FOR RESIDUE EDO O 17
09
AC9
SOFTWARE
ARG O:269 , GLU P:352 , LYS P:370 , HOH P:502
BINDING SITE FOR RESIDUE EDO O 18
10
BC1
SOFTWARE
HOH P:19 , HOH P:28 , HOH P:55 , HOH P:60 , HOH P:62 , ASN P:81 , GLY P:82 , PHE P:83 , GLY P:84 , ARG P:85 , ILE P:86 , ASP P:106 , PRO P:107 , PHE P:108 , LYS P:151 , SER P:169 , THR P:170 , GLY P:171 , TYR P:173 , SER P:193 , ALA P:194 , ALA P:255 , PRO P:263 , ASN P:388 , TYR P:392 , PO4 P:415 , HOH P:489 , HOH P:511 , HOH P:531 , HOH P:545 , HOH P:549 , HOH P:586 , HOH P:596 , HOH P:607 , HOH P:608 , HOH P:609
BINDING SITE FOR RESIDUE NAD P 1
11
BC2
SOFTWARE
NAD P:1 , HOH P:60 , THR P:254 , THR P:256 , ARG P:306 , HOH P:434 , HOH P:436 , HOH P:510 , HOH P:549 , HOH P:581 , HOH P:622
BINDING SITE FOR RESIDUE PO4 P 415
12
BC3
SOFTWARE
SER P:223 , CYS P:224 , THR P:225 , HIS P:251 , THR P:283 , GLY P:284 , ARG P:306 , HOH P:436 , HOH P:495 , HOH P:549 , HOH P:614 , HOH P:622
BINDING SITE FOR RESIDUE PO4 P 3
13
BC4
SOFTWARE
ARG O:126 , HOH O:506 , PHE P:358 , ASP P:361
BINDING SITE FOR RESIDUE EDO P 5
14
BC5
SOFTWARE
ALA P:267 , TRP P:268 , HOH P:620
BINDING SITE FOR RESIDUE EDO P 6
15
BC6
SOFTWARE
PRO P:200 , MET P:201 , ASN P:207 , HOH P:593 , HOH P:625
BINDING SITE FOR RESIDUE EDO P 7
16
BC7
SOFTWARE
VAL P:206 , ASN P:207 , GLU P:208 , ASN P:209
BINDING SITE FOR RESIDUE EDO P 10
17
BC8
SOFTWARE
PHE O:358 , ASP O:361 , ARG P:126 , HOH P:494
BINDING SITE FOR RESIDUE EDO P 11
18
BC9
SOFTWARE
EDO P:13 , ALA P:369 , GLY P:372 , HOH P:616
BINDING SITE FOR RESIDUE EDO P 12
19
CC1
SOFTWARE
EDO P:12 , LYS P:331 , LYS P:370
BINDING SITE FOR RESIDUE EDO P 13
20
CC2
SOFTWARE
PRO P:197 , LYS P:291 , PRO P:324 , PRO P:326 , ASP P:377 , HOH P:593
BINDING SITE FOR RESIDUE EDO P 16
[
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SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_049219 (D110N, chain O/P, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_049219
D
110
N
G3PT_HUMAN
Polymorphism
2285514
O/P
D
110
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (O:222-229,P:222-229)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GAPDH
PS00071
Glyceraldehyde 3-phosphate dehydrogenase active site.
G3PT_HUMAN
222-229
4
O:222-229
P:222-229
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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_3h9eA02 (A:222-388)
1b: CATH_3h9eB02 (B:222-388)
2a: CATH_3h9eB01 (B:74-221,B:389-410)
2b: CATH_3h9eA01 (A:74-221,A:389-409)
View:
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Classes
(
)
(
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Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Human (Homo sapiens)
(8)
1a
3h9eA02
A:222-388
1b
3h9eB02
B:222-388
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
3h9eB01
B:74-221,B:389-410
2b
3h9eA01
A:74-221,A:389-409
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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Atom Selection
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Protein & NOT Site
Protein & NOT PROSITE
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Asymmetric Unit 1
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