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1T2F
Biol. Unit 1
Info
Asym.Unit (226 KB)
Biol.Unit 1 (215 KB)
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(1)
Title
:
HUMAN B LACTATE DEHYDROGENASE COMPLEXED WITH NAD+ AND 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID
Authors
:
A. Cameron, J. Read, R. Tranter, V. J. Winter, R. B. Sessions, R. L. Brady, L. Vivas, A. Easton, H. Kendrick, S. L. Croft, D. Barros, J. L. Lavandera, J. J. Martin, F. Risco, S. Garcia-Ochoa, F. J. Gamo, L. Sanz, L. Leon, J. R. Ruiz, R. Gabarro, A. Mallo, F. G. De Las Heras
Date
:
21 Apr 04 (Deposition) - 11 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Protein-Ligand Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Cameron, J. Read, R. Tranter, V. J. Winter, R. B. Sessions, R. L. Brady, L. Vivas, A. Easton, H. Kendrick, S. L. Croft, D. Barros, J. L. Lavandera, J. J. Martin, F. Risco, S. Garcia-Ochoa, F. J. Gamo, L. Sanz, L. Leon, J. R. Ruiz, R. Gabarro, A. Mallo, F. G. De Las Heras
Identification And Activity Of A Series Of Azole-Based Compounds With Lactate Dehydrogenase-Directed Anti-Malarial Activity.
J. Biol. Chem. V. 279 31429 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2a: 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBO... (OXQa)
2b: 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBO... (OXQb)
2c: 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBO... (OXQc)
2d: 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBO... (OXQd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
OXQ
4
Ligand/Ion
4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:29 , GLN A:30 , VAL A:31 , ASP A:52 , VAL A:53 , LEU A:54 , TYR A:83 , THR A:95 , GLY A:97 , VAL A:98 , ARG A:99 , VAL A:116 , ILE A:120 , VAL A:136 , SER A:137 , ASN A:138 , SER A:161 , HIS A:193 , THR A:248 , ILE A:252 , OXQ A:402 , HOH A:433 , HOH A:434
BINDING SITE FOR RESIDUE NAD A 401
2
AC2
SOFTWARE
GLN A:100 , ARG A:106 , ASN A:138 , LEU A:165 , ARG A:169 , HIS A:193 , THR A:248 , NAD A:401
BINDING SITE FOR RESIDUE OXQ A 402
3
AC3
SOFTWARE
VAL B:28 , GLY B:29 , GLN B:30 , VAL B:31 , ASP B:52 , VAL B:53 , LEU B:54 , THR B:95 , ALA B:96 , GLY B:97 , VAL B:98 , ARG B:99 , GLN B:100 , ILE B:120 , VAL B:136 , SER B:137 , ASN B:138 , SER B:161 , HIS B:193 , THR B:248 , ILE B:252 , OXQ B:404 , HOH B:424 , HOH B:473 , HOH B:480 , ASN D:108
BINDING SITE FOR RESIDUE NAD B 403
4
AC4
SOFTWARE
GLN B:100 , ARG B:106 , ASN B:138 , ARG B:169 , HIS B:193 , THR B:248 , NAD B:403 , HOH B:480
BINDING SITE FOR RESIDUE OXQ B 404
5
AC5
SOFTWARE
ASN A:108 , VAL C:28 , GLY C:29 , GLN C:30 , VAL C:31 , ASP C:52 , VAL C:53 , LEU C:54 , THR C:95 , ALA C:96 , GLY C:97 , VAL C:98 , ARG C:99 , VAL C:116 , VAL C:136 , ASN C:138 , SER C:161 , HIS C:193 , THR C:248 , ILE C:252 , OXQ C:406 , HOH C:419 , HOH C:427 , HOH C:437
BINDING SITE FOR RESIDUE NAD C 405
6
AC6
SOFTWARE
GLN C:100 , ARG C:106 , ASN C:138 , LEU C:165 , ARG C:169 , HIS C:193 , ALA C:238 , THR C:248 , NAD C:405 , HOH C:419
BINDING SITE FOR RESIDUE OXQ C 406
7
AC7
SOFTWARE
GLY D:29 , GLN D:30 , VAL D:31 , ASP D:52 , VAL D:53 , LEU D:54 , THR D:95 , ALA D:96 , GLY D:97 , VAL D:98 , ARG D:99 , VAL D:136 , ASN D:138 , SER D:161 , LEU D:165 , HIS D:193 , THR D:248 , ILE D:252 , OXQ D:408 , HOH D:419 , HOH D:420 , HOH D:443 , HOH D:444
BINDING SITE FOR RESIDUE NAD D 407
8
AC8
SOFTWARE
GLN D:100 , ARG D:106 , ASN D:138 , LEU D:165 , ARG D:169 , HIS D:193 , ALA D:238 , THR D:248 , NAD D:407 , HOH D:419
BINDING SITE FOR RESIDUE OXQ D 408
[
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]
SAPs(SNPs)/Variants
(12, 48)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_004173 (K6E, chain A/B/C/D, )
02: VAR_004174 (A34E, chain A/B/C/D, )
03: VAR_011634 (G68E, chain A/B/C/D, )
04: VAR_011635 (R106W, chain A/B/C/D, )
05: VAR_004175 (S128R, chain A/B/C/D, )
06: VAR_004176 (F170V, chain A/B/C/D, )
07: VAR_004177 (R171H, chain A/B/C/D, )
08: VAR_011636 (R171P, chain A/B/C/D, )
09: VAR_004178 (M174L, chain A/B/C/D, )
10: VAR_049758 (M174V, chain A/B/C/D, )
11: VAR_004179 (D321V, chain A/B/C/D, )
12: VAR_011638 (W324R, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_004173
K
7
E
LDHB_HUMAN
Unclassified
---
A/B/C/D
K
6
E
02
UniProt
VAR_004174
A
35
E
LDHB_HUMAN
Unclassified
---
A/B/C/D
A
34
E
03
UniProt
VAR_011634
G
69
E
LDHB_HUMAN
Unclassified
---
A/B/C/D
G
68
E
04
UniProt
VAR_011635
R
107
W
LDHB_HUMAN
Unclassified
---
A/B/C/D
R
106
W
05
UniProt
VAR_004175
S
129
R
LDHB_HUMAN
Unclassified
---
A/B/C/D
S
128
R
06
UniProt
VAR_004176
F
171
V
LDHB_HUMAN
Unclassified
---
A/B/C/D
F
170
V
07
UniProt
VAR_004177
R
172
H
LDHB_HUMAN
Unclassified
---
A/B/C/D
R
171
H
08
UniProt
VAR_011636
R
172
P
LDHB_HUMAN
Unclassified
---
A/B/C/D
R
171
P
09
UniProt
VAR_004178
M
175
L
LDHB_HUMAN
Unclassified
---
A/B/C/D
M
174
L
10
UniProt
VAR_049758
M
175
V
LDHB_HUMAN
Polymorphism
7966339
A/B/C/D
M
174
V
11
UniProt
VAR_004179
D
322
V
LDHB_HUMAN
Unclassified
---
A/B/C/D
D
321
V
12
UniProt
VAR_011638
W
325
R
LDHB_HUMAN
Unclassified
---
A/B/C/D
W
324
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: L_LDH (A:190-196,B:190-196,C:190-196,D:19...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
L_LDH
PS00064
L-lactate dehydrogenase active site.
LDHB_HUMAN
191-197
4
A:190-196
B:190-196
C:190-196
D:190-196
[
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1t2fa2 (A:161-332)
1b: SCOP_d1t2fb2 (B:161-332)
1c: SCOP_d1t2fc2 (C:161-332)
1d: SCOP_d1t2fd2 (D:161-332)
2a: SCOP_d1t2fa1 (A:1-160)
2b: SCOP_d1t2fb1 (B:1-160)
2c: SCOP_d1t2fc1 (C:1-160)
2d: SCOP_d1t2fd1 (D:1-160)
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)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
Lactate & malate dehydrogenases, C-terminal domain
(125)
Protein domain
:
Lactate dehydrogenase
(55)
Human (Homo sapiens), heart isoform (H chain) [TaxId: 9606]
(2)
1a
d1t2fa2
A:161-332
1b
d1t2fb2
B:161-332
1c
d1t2fc2
C:161-332
1d
d1t2fd2
D:161-332
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
:
LDH N-terminal domain-like
(117)
Protein domain
:
Lactate dehydrogenase
(53)
Human (Homo sapiens), heart isoform (H chain) [TaxId: 9606]
(2)
2a
d1t2fa1
A:1-160
2b
d1t2fb1
B:1-160
2c
d1t2fc1
C:1-160
2d
d1t2fd1
D:1-160
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1t2fA01 (A:15-162)
1b: CATH_1t2fB01 (B:15-162)
1c: CATH_1t2fC01 (C:15-162)
1d: CATH_1t2fD01 (D:15-162)
2a: CATH_1t2fA02 (A:163-330)
2b: CATH_1t2fB02 (B:163-330)
2c: CATH_1t2fC02 (C:163-330)
2d: CATH_1t2fD02 (D:163-330)
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(
)
(
)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
1t2fA01
A:15-162
1b
1t2fB01
B:15-162
1c
1t2fC01
C:15-162
1d
1t2fD01
D:15-162
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
(116)
Homologous Superfamily
:
L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2
(116)
Human (Homo sapiens)
(4)
2a
1t2fA02
A:163-330
2b
1t2fB02
B:163-330
2c
1t2fC02
C:163-330
2d
1t2fD02
D:163-330
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Ldh_1_C_1t2fD01 (D:163-331)
1b: PFAM_Ldh_1_C_1t2fD02 (D:163-331)
1c: PFAM_Ldh_1_C_1t2fD03 (D:163-331)
1d: PFAM_Ldh_1_C_1t2fD04 (D:163-331)
2a: PFAM_Ldh_1_N_1t2fD05 (D:21-161)
2b: PFAM_Ldh_1_N_1t2fD06 (D:21-161)
2c: PFAM_Ldh_1_N_1t2fD07 (D:21-161)
2d: PFAM_Ldh_1_N_1t2fD08 (D:21-161)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LDH_C
(56)
Family
:
Ldh_1_C
(51)
Homo sapiens (Human)
(1)
1a
Ldh_1_C-1t2fD01
D:163-331
1b
Ldh_1_C-1t2fD02
D:163-331
1c
Ldh_1_C-1t2fD03
D:163-331
1d
Ldh_1_C-1t2fD04
D:163-331
Clan
:
NADP_Rossmann
(1239)
Family
:
Ldh_1_N
(51)
Homo sapiens (Human)
(1)
2a
Ldh_1_N-1t2fD05
D:21-161
2b
Ldh_1_N-1t2fD06
D:21-161
2c
Ldh_1_N-1t2fD07
D:21-161
2d
Ldh_1_N-1t2fD08
D:21-161
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