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1T2F
Asym. Unit
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 not available)
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)
[
close SNP/Variant info
]
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:
Select:
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
[
close PROSITE info
]
Exons
(7, 28)
Info
All Exons
Exon 1.4a (A:1-42 | B:1-42 | C:1-42 | D:1-42)
Exon 1.5 (A:43-82 | B:43-82 | C:43-82 | D:43...)
Exon 1.6b (A:82-140 | B:82-140 | C:82-140 | D...)
Exon 1.7 (A:140-198 | B:140-198 | C:140-198 ...)
Exon 1.8b (A:198-237 | B:198-237 | C:198-237 ...)
Exon 1.9 (A:237-278 | B:237-278 | C:237-278 ...)
Exon 1.10b (A:279-332 | B:279-332 | C:279-332 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1d/1.4a
2: Boundary 1.4a/1.5
3: Boundary 1.5/1.6b
4: Boundary 1.6b/1.7
5: Boundary 1.7/1.8b
6: Boundary 1.8b/1.9
7: Boundary 1.9/1.10b
8: Boundary 1.10b/-
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
1.1d
ENST00000396076
1d
ENSE00001523775
chr12:
21810728-21810402
327
LDHB_HUMAN
-
0
0
-
-
1.4a
ENST00000396076
4a
ENSE00000822271
chr12:
21807611-21807477
135
LDHB_HUMAN
1-43
43
4
A:1-42
B:1-42
C:1-42
D:1-42
42
42
42
42
1.5
ENST00000396076
5
ENSE00000726205
chr12:
21799950-21799833
118
LDHB_HUMAN
44-83
40
4
A:43-82
B:43-82
C:43-82
D:43-82
40
40
40
40
1.6b
ENST00000396076
6b
ENSE00000726202
chr12:
21797042-21796869
174
LDHB_HUMAN
83-141
59
4
A:82-140
B:82-140
C:82-140
D:82-140
59
59
59
59
1.7
ENST00000396076
7
ENSE00000726197
chr12:
21795059-21794886
174
LDHB_HUMAN
141-199
59
4
A:140-198
B:140-198
C:140-198
D:140-198
59
59
59
59
1.8b
ENST00000396076
8b
ENSE00000726193
chr12:
21791404-21791287
118
LDHB_HUMAN
199-238
40
4
A:198-237
B:198-237
C:198-237
D:198-237
40
40
40
40
1.9
ENST00000396076
9
ENSE00000726188
chr12:
21790128-21790005
124
LDHB_HUMAN
238-279
42
4
A:237-278
B:237-278
C:237-278
D:237-278
42
42
42
42
1.10b
ENST00000396076
10b
ENSE00000994921
chr12:
21788643-21788276
368
LDHB_HUMAN
280-334
55
4
A:279-332
B:279-332
C:279-332
D:279-332
54
54
54
54
[
close EXON info
]
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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)
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
[
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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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)
(
)
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
[
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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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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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