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Getting 'Biological Unit' information from database.
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3H9E
Asym. Unit
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, 20)
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
14
Ligand/Ion
1,2-ETHANEDIOL
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
PO4
4
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, 2)
Info
(mutated residues are not available)
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, 2)
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
2
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.
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
(
)
(
)
Architectures
(
)
(
)
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 Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain O
Chain P
Asymmetric Unit 1
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