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3H3F
Biol. Unit 2
Info
Asym.Unit (455 KB)
Biol.Unit 1 (225 KB)
Biol.Unit 2 (226 KB)
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(1)
Title
:
RABBIT MUSCLE L-LACTATE DEHYDROGENASE IN COMPLEX WITH NADH AND OXAMATE
Authors
:
A. Bujacz, G. Bujacz, K. Swiderek, P. Paneth
Date
:
16 Apr 09 (Deposition) - 15 Sep 09 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.38
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Dehydrogenase, Rossmann Fold, Oxidoreductase, Glycolysis, Nad, Nadh, Oxamate, M-Type Tetramer
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Swiderek, A. Panczakiewicz, A. Bujacz, G. Bujacz, P. Paneth
Modeling Of Isotope Effects On Binding Oxamate To Lactic Dehydrogenase
J. Phys. Chem. B V. 113 12782 2009
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close entry info
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Hetero Components
(3, 22)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
1j: ACETATE ION (ACTj)
1k: ACETATE ION (ACTk)
1l: ACETATE ION (ACTl)
1m: ACETATE ION (ACTm)
1n: ACETATE ION (ACTn)
1o: ACETATE ION (ACTo)
1p: ACETATE ION (ACTp)
1q: ACETATE ION (ACTq)
1r: ACETATE ION (ACTr)
1s: ACETATE ION (ACTs)
1t: ACETATE ION (ACTt)
1u: ACETATE ION (ACTu)
1v: ACETATE ION (ACTv)
1w: ACETATE ION (ACTw)
2a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
2b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
2c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
2d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
2e: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIe)
2f: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIf)
2g: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIg)
2h: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIh)
3a: OXAMIC ACID (OXMa)
3b: OXAMIC ACID (OXMb)
3c: OXAMIC ACID (OXMc)
3d: OXAMIC ACID (OXMd)
3e: OXAMIC ACID (OXMe)
3f: OXAMIC ACID (OXMf)
3g: OXAMIC ACID (OXMg)
3h: OXAMIC ACID (OXMh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
14
Ligand/Ion
ACETATE ION
2
NAI
4
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3
OXM
4
Ligand/Ion
OXAMIC ACID
[
close Hetero Component info
]
Sites
(23, 23)
Info
All Sites
01: AC1 (SOFTWARE)
02: BC9 (SOFTWARE)
03: CC1 (SOFTWARE)
04: CC2 (SOFTWARE)
05: CC3 (SOFTWARE)
06: CC4 (SOFTWARE)
07: CC5 (SOFTWARE)
08: CC6 (SOFTWARE)
09: CC7 (SOFTWARE)
10: CC8 (SOFTWARE)
11: CC9 (SOFTWARE)
12: DC1 (SOFTWARE)
13: DC2 (SOFTWARE)
14: DC3 (SOFTWARE)
15: DC4 (SOFTWARE)
16: DC5 (SOFTWARE)
17: DC6 (SOFTWARE)
18: DC7 (SOFTWARE)
19: DC8 (SOFTWARE)
20: DC9 (SOFTWARE)
21: EC1 (SOFTWARE)
22: EC2 (SOFTWARE)
23: EC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:28 , ALA A:29 , VAL A:30 , ASP A:51 , VAL A:52 , MET A:53 , THR A:94 , ALA A:95 , GLY A:96 , ILE A:115 , VAL A:135 , SER A:136 , ASN A:137 , HIS A:192 , ILE A:251 , OXM A:333 , HOH A:335 , HOH A:359 , HOH A:1075 , HOH A:1095 , HOH A:1117 , GLY E:102
BINDING SITE FOR RESIDUE NAI A 332
02
BC9
SOFTWARE
GLY E:28 , ALA E:29 , VAL E:30 , ASP E:51 , VAL E:52 , MET E:53 , THR E:94 , ALA E:95 , GLY E:96 , ILE E:115 , VAL E:135 , ASN E:137 , HIS E:192 , THR E:247 , ILE E:251 , OXM E:333 , HOH E:433 , HOH E:568 , HOH E:1054
BINDING SITE FOR RESIDUE NAI E 332
03
CC1
SOFTWARE
ASN E:137 , LEU E:164 , ARG E:168 , HIS E:192 , ALA E:237 , THR E:247 , NAI E:332
BINDING SITE FOR RESIDUE OXM E 333
04
CC2
SOFTWARE
LEU E:182 , HIS E:185 , HOH E:357 , HOH E:532 , ARG G:170
BINDING SITE FOR RESIDUE ACT E 334
05
CC3
SOFTWARE
ASP E:42 , PHE E:70
BINDING SITE FOR RESIDUE ACT E 335
06
CC4
SOFTWARE
ARG E:267 , HOH E:884
BINDING SITE FOR RESIDUE ACT E 336
07
CC5
SOFTWARE
LYS E:242
BINDING SITE FOR RESIDUE ACT E 337
08
CC6
SOFTWARE
ASP E:42 , ASP H:42 , ACT H:337
BINDING SITE FOR RESIDUE ACT E 338
09
CC7
SOFTWARE
ASN B:107 , GLY F:28 , ALA F:29 , VAL F:30 , ASP F:51 , VAL F:52 , MET F:53 , LYS F:56 , THR F:94 , ALA F:95 , GLY F:96 , ALA F:97 , ARG F:98 , VAL F:135 , ASN F:137 , SER F:160 , HIS F:192 , THR F:247 , ILE F:251 , OXM F:333 , HOH F:341 , HOH F:343 , HOH F:351 , HOH F:352 , HOH F:353 , HOH F:390 , HOH F:395 , HOH F:447 , HOH F:1065
BINDING SITE FOR RESIDUE NAI F 332
10
CC8
SOFTWARE
GLN F:99 , ARG F:105 , ASN F:137 , ARG F:168 , HIS F:192 , ALA F:237 , THR F:247 , NAI F:332
BINDING SITE FOR RESIDUE OXM F 333
11
CC9
SOFTWARE
MET F:40 , PHE F:70 , ARG F:72
BINDING SITE FOR RESIDUE ACT F 334
12
DC1
SOFTWARE
HIS F:16 , HOH F:1191
BINDING SITE FOR RESIDUE ACT F 335
13
DC2
SOFTWARE
GLY G:28 , ALA G:29 , VAL G:30 , ASP G:51 , MET G:53 , LYS G:56 , THR G:94 , ALA G:95 , GLY G:96 , ALA G:97 , ARG G:98 , ILE G:119 , VAL G:135 , SER G:136 , ASN G:137 , SER G:160 , HIS G:192 , THR G:247 , ILE G:251 , OXM G:333 , HOH G:347 , HOH G:350 , HOH G:354 , HOH G:367 , HOH G:369 , HOH G:378 , HOH G:717
BINDING SITE FOR RESIDUE NAI G 332
14
DC3
SOFTWARE
GLN G:99 , ARG G:105 , ASN G:137 , ARG G:168 , HIS G:192 , ALA G:237 , THR G:247 , NAI G:332
BINDING SITE FOR RESIDUE OXM G 333
15
DC4
SOFTWARE
ASP G:42 , PHE G:70 , LEU G:71 , ARG G:72
BINDING SITE FOR RESIDUE ACT G 334
16
DC5
SOFTWARE
LEU G:213 , HIS G:214 , PRO G:215 , LYS G:223 , GLN H:6
BINDING SITE FOR RESIDUE ACT G 335
17
DC6
SOFTWARE
LEU G:329 , GLN G:330 , PHE G:331
BINDING SITE FOR RESIDUE ACT G 336
18
DC7
SOFTWARE
GLN D:330 , GLY H:28 , ALA H:29 , VAL H:30 , ASP H:51 , VAL H:52 , MET H:53 , THR H:94 , ALA H:95 , GLY H:96 , ARG H:98 , ILE H:115 , VAL H:135 , ASN H:137 , HIS H:192 , THR H:247 , OXM H:333 , HOH H:341 , HOH H:344 , HOH H:369 , HOH H:372 , HOH H:572 , HOH H:849
BINDING SITE FOR RESIDUE NAI H 332
19
DC8
SOFTWARE
ASN H:137 , ARG H:168 , HIS H:192 , ALA H:237 , THR H:247 , NAI H:332
BINDING SITE FOR RESIDUE OXM H 333
20
DC9
SOFTWARE
VAL H:305 , HOH H:853
BINDING SITE FOR RESIDUE ACT H 334
21
EC1
SOFTWARE
MET H:40 , ASP H:42
BINDING SITE FOR RESIDUE ACT H 335
22
EC2
SOFTWARE
LYS H:4
BINDING SITE FOR RESIDUE ACT H 336
23
EC3
SOFTWARE
ACT E:338 , LYS H:41 , GLU H:260
BINDING SITE FOR RESIDUE ACT H 337
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: L_LDH (E:189-195,F:189-195,G:189-195,H:18...)
;
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.
LDHA_RABIT
190-196
4
-
-
-
-
E:189-195
F:189-195
G:189-195
H:189-195
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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, 16)
Info
All SCOP Domains
1a: SCOP_d3h3fa2 (A:160-331)
1b: SCOP_d3h3fb2 (B:160-331)
1c: SCOP_d3h3fc2 (C:160-331)
1d: SCOP_d3h3fd2 (D:160-331)
1e: SCOP_d3h3fe2 (E:160-331)
1f: SCOP_d3h3ff2 (F:160-331)
1g: SCOP_d3h3fg2 (G:160-331)
1h: SCOP_d3h3fh2 (H:160-331)
2a: SCOP_d3h3fa1 (A:1-159)
2b: SCOP_d3h3fb1 (B:1-159)
2c: SCOP_d3h3fc1 (C:1-159)
2d: SCOP_d3h3fd1 (D:1-159)
2e: SCOP_d3h3fe1 (E:1-159)
2f: SCOP_d3h3ff1 (F:1-159)
2g: SCOP_d3h3fg1 (G:1-159)
2h: SCOP_d3h3fh1 (H:1-159)
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)
(
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Families
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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
:
automated matches
(30)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(5)
1a
d3h3fa2
A:160-331
1b
d3h3fb2
B:160-331
1c
d3h3fc2
C:160-331
1d
d3h3fd2
D:160-331
1e
d3h3fe2
E:160-331
1f
d3h3ff2
F:160-331
1g
d3h3fg2
G:160-331
1h
d3h3fh2
H:160-331
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
:
automated matches
(15)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(5)
2a
d3h3fa1
A:1-159
2b
d3h3fb1
B:1-159
2c
d3h3fc1
C:1-159
2d
d3h3fd1
D:1-159
2e
d3h3fe1
E:1-159
2f
d3h3ff1
F:1-159
2g
d3h3fg1
G:1-159
2h
d3h3fh1
H:1-159
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
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Sorry, no Info available
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