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1ZNQ
Asym. Unit
Info
Asym.Unit (215 KB)
Biol.Unit 1 (209 KB)
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(1)
Title
:
CRSYTAL STRUCTURE OF HUMAN LIVER GAPDH
Authors
:
S. A. Ismail, H. W. Park
Date
:
11 May 05 (Deposition) - 24 May 05 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : O,P,Q,R
Biol. Unit 1: O,P,Q,R (1x)
Keywords
:
Rossmann Fold, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. A. Ismail, H. W. Park
Crystal Structure Analysis Of Human Liver Gapdh
To Be Published
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN O:9 , GLY O:10 , PHE O:11 , GLY O:12 , ARG O:13 , ILE O:14 , ASN O:34 , ASP O:35 , PRO O:36 , PHE O:37 , ILE O:38 , ARG O:80 , SER O:98 , THR O:99 , GLY O:100 , PHE O:102 , SER O:122 , ALA O:123 , CYS O:152 , ASN O:316 , HOH O:1010
BINDING SITE FOR RESIDUE NAD O 1001
2
AC2
SOFTWARE
ASN P:9 , GLY P:10 , PHE P:11 , GLY P:12 , ARG P:13 , ILE P:14 , ASP P:35 , PRO P:36 , PHE P:37 , ILE P:38 , ARG P:80 , SER P:98 , THR P:99 , GLY P:100 , SER P:122 , ALA P:123 , CYS P:152 , ASN P:316 , GLU P:317 , TYR P:320 , HOH P:1009 , HOH P:1033
BINDING SITE FOR RESIDUE NAD P 1002
3
AC3
SOFTWARE
ASN R:9 , GLY R:10 , PHE R:11 , GLY R:12 , ARG R:13 , ILE R:14 , ASP R:35 , PRO R:36 , PHE R:37 , ILE R:38 , ARG R:80 , SER R:98 , THR R:99 , GLY R:100 , SER R:122 , ALA R:123 , CYS R:152 , ALA R:183 , ASN R:316 , TYR R:320 , HOH R:1006 , HOH R:1020
BINDING SITE FOR RESIDUE NAD R 1003
4
AC4
SOFTWARE
ASN Q:9 , GLY Q:10 , PHE Q:11 , GLY Q:12 , ARG Q:13 , ILE Q:14 , ASP Q:35 , PRO Q:36 , PHE Q:37 , ILE Q:38 , ARG Q:80 , SER Q:98 , THR Q:99 , GLY Q:100 , PHE Q:102 , SER Q:122 , ALA Q:123 , CYS Q:152 , ASN Q:316 , GLU Q:317 , TYR Q:320
BINDING SITE FOR RESIDUE NAD Q 1004
[
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]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_018889 (A22G, chain O/P/Q/R, )
2: VAR_049218 (K251N, chain O/P/Q/R, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_018889
A
22
G
G3P_HUMAN
Polymorphism
45541435
O/P/Q/R
A
22
G
2
UniProt
VAR_049218
K
251
N
G3P_HUMAN
Polymorphism
1062429
O/P/Q/R
K
251
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (O:150-157,P:150-157,Q:150-157,R:15...)
;
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.
G3P_HUMAN
150-157
4
O:150-157
P:150-157
Q:150-157
R:150-157
[
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]
Exons
(8, 32)
Info
All Exons
Exon 1.2c (O:3-10 | P:3-10 | Q:3-10 | R:3-10)
Exon 1.4 (O:10-43 | P:10-43 | Q:10-43 | R:10...)
Exon 1.5a (O:44-79 | P:44-79 | Q:44-79 | R:44...)
Exon 1.5g (O:79-109 | P:79-109 | Q:79-109 | R...)
Exon 1.5h (O:110-148 | P:110-148 | Q:110-148 ...)
Exon 1.5j (O:148-175 | P:148-175 | Q:148-175 ...)
Exon 1.5n (O:176-313 | P:176-313 | Q:176-313 ...)
Exon 1.6h (O:313-335 | P:313-335 | Q:313-335 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1f/1.2c
2: Boundary 1.2c/1.4
3: Boundary 1.4/1.5a
4: Boundary 1.5a/1.5g
5: Boundary 1.5g/1.5h
6: Boundary 1.5h/1.5j
7: Boundary 1.5j/1.5n
8: Boundary 1.5n/1.6h
9: Boundary 1.6h/-
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
1.1f
ENST00000396861
1f
ENSE00001526521
chr12:
6643700-6643827
128
G3P_HUMAN
-
0
0
-
-
1.2c
ENST00000396861
2c
ENSE00002166923
chr12:
6643976-6644027
52
G3P_HUMAN
1-10
10
4
O:3-10
P:3-10
Q:3-10
R:3-10
8
8
8
8
1.4
ENST00000396861
4
ENSE00001682256
chr12:
6645660-6645759
100
G3P_HUMAN
10-43
34
4
O:10-43
P:10-43
Q:10-43
R:10-43
34
34
34
34
1.5a
ENST00000396861
5a
ENSE00001675799
chr12:
6645850-6645956
107
G3P_HUMAN
44-79
36
4
O:44-79
P:44-79
Q:44-79
R:44-79
36
36
36
36
1.5g
ENST00000396861
5g
ENSE00001803982
chr12:
6646086-6646176
91
G3P_HUMAN
79-109
31
4
O:79-109
P:79-109
Q:79-109
R:79-109
31
31
31
31
1.5h
ENST00000396861
5h
ENSE00001619556
chr12:
6646267-6646382
116
G3P_HUMAN
110-148
39
4
O:110-148
P:110-148
Q:110-148
R:110-148
39
39
39
39
1.5j
ENST00000396861
5j
ENSE00001763432
chr12:
6646475-6646556
82
G3P_HUMAN
148-175
28
4
O:148-175
P:148-175
Q:148-175
R:148-175
28
28
28
28
1.5n
ENST00000396861
5n
ENSE00000715225
chr12:
6646750-6647162
413
G3P_HUMAN
176-313
138
4
O:176-313
P:176-313
Q:176-313
R:176-313
138
138
138
138
1.6h
ENST00000396861
6h
ENSE00001526518
chr12:
6647267-6647525
259
G3P_HUMAN
313-335
23
4
O:313-335
P:313-335
Q:313-335
R:313-335
23
23
23
23
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1znqo2 (O:152-315)
1b: SCOP_d1znqp2 (P:152-315)
1c: SCOP_d1znqq2 (Q:152-315)
1d: SCOP_d1znqr2 (R:152-315)
2a: SCOP_d1znqo1 (O:3-151,O:316-335)
2b: SCOP_d1znqp1 (P:3-151,P:316-335)
2c: SCOP_d1znqq1 (Q:3-151,Q:316-335)
2d: SCOP_d1znqr1 (R:3-151,R:316-335)
View:
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(
)
(
)
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(
)
(
)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
GAPDH-like
(99)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Human (Homo sapiens), liver isoform [TaxId: 9606]
(2)
1a
d1znqo2
O:152-315
1b
d1znqp2
P:152-315
1c
d1znqq2
Q:152-315
1d
d1znqr2
R:152-315
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Human (Homo sapiens), liver isoform [TaxId: 9606]
(2)
2a
d1znqo1
O:3-151,O:316-335
2b
d1znqp1
P:3-151,P:316-335
2c
d1znqq1
Q:3-151,Q:316-335
2d
d1znqr1
R:3-151,R:316-335
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1znqO02 (O:150-316)
1b: CATH_1znqP02 (P:150-316)
1c: CATH_1znqQ02 (Q:150-316)
1d: CATH_1znqR02 (R:150-316)
2a: CATH_1znqO01 (O:3-149,O:317-335)
2b: CATH_1znqP01 (P:3-149,P:317-335)
2c: CATH_1znqQ01 (Q:3-149,Q:317-335)
2d: CATH_1znqR01 (R:3-149,R:317-335)
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
1znqO02
O:150-316
1b
1znqP02
P:150-316
1c
1znqQ02
Q:150-316
1d
1znqR02
R:150-316
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
1znqO01
O:3-149,O:317-335
2b
1znqP01
P:3-149,P:317-335
2c
1znqQ01
Q:3-149,Q:317-335
2d
1znqR01
R:3-149,R:317-335
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_1znqR01 (R:157-314)
1b: PFAM_Gp_dh_C_1znqR02 (R:157-314)
1c: PFAM_Gp_dh_C_1znqR03 (R:157-314)
1d: PFAM_Gp_dh_C_1znqR04 (R:157-314)
2a: PFAM_Gp_dh_N_1znqR05 (R:4-152)
2b: PFAM_Gp_dh_N_1znqR06 (R:4-152)
2c: PFAM_Gp_dh_N_1znqR07 (R:4-152)
2d: PFAM_Gp_dh_N_1znqR08 (R:4-152)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GADPH_aa-bio_dh
(59)
Family
:
Gp_dh_C
(38)
Homo sapiens (Human)
(3)
1a
Gp_dh_C-1znqR01
R:157-314
1b
Gp_dh_C-1znqR02
R:157-314
1c
Gp_dh_C-1znqR03
R:157-314
1d
Gp_dh_C-1znqR04
R:157-314
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Homo sapiens (Human)
(3)
2a
Gp_dh_N-1znqR05
R:4-152
2b
Gp_dh_N-1znqR06
R:4-152
2c
Gp_dh_N-1znqR07
R:4-152
2d
Gp_dh_N-1znqR08
R:4-152
[
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Asym.Unit (215 KB)
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