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3H3F
Asym. Unit
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
[
close entry info
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Hetero Components
(3, 39)
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
23
Ligand/Ion
ACETATE ION
2
NAI
8
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3
OXM
8
Ligand/Ion
OXAMIC ACID
[
close Hetero Component info
]
Sites
(39, 39)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: 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
AC2
SOFTWARE
ASN A:137 , ARG A:168 , HIS A:192 , ALA A:237 , THR A:247 , NAI A:332
BINDING SITE FOR RESIDUE OXM A 333
03
AC3
SOFTWARE
ASP A:42 , PHE A:70 , ARG A:72
BINDING SITE FOR RESIDUE ACT A 334
04
AC4
SOFTWARE
GLY B:28 , ALA B:29 , VAL B:30 , ASP B:51 , VAL B:52 , MET B:53 , LYS B:56 , THR B:94 , ALA B:95 , GLY B:96 , ALA B:97 , ARG B:98 , VAL B:135 , ASN B:137 , LEU B:164 , HIS B:192 , THR B:247 , ILE B:251 , OXM B:333 , HOH B:336 , HOH B:339 , HOH B:344 , HOH B:347 , HOH B:364 , HOH B:365 , HOH B:422
BINDING SITE FOR RESIDUE NAI B 332
05
AC5
SOFTWARE
GLN B:99 , ARG B:105 , ASN B:137 , ARG B:168 , HIS B:192 , ALA B:237 , THR B:247 , NAI B:332
BINDING SITE FOR RESIDUE OXM B 333
06
AC6
SOFTWARE
LYS B:304 , VAL B:305 , HOH B:392 , HOH B:394
BINDING SITE FOR RESIDUE ACT B 334
07
AC7
SOFTWARE
GLY C:28 , ALA C:29 , VAL C:30 , ASP C:51 , VAL C:52 , MET C:53 , LYS C:56 , THR C:94 , ALA C:95 , GLY C:96 , ALA C:97 , ARG C:98 , ILE C:119 , VAL C:135 , ASN C:137 , SER C:160 , HIS C:192 , THR C:247 , ILE C:251 , OXM C:333 , HOH C:351 , HOH C:352 , HOH C:366 , HOH C:368 , HOH C:555 , HOH C:729 , HOH C:730 , HOH C:776
BINDING SITE FOR RESIDUE NAI C 332
08
AC8
SOFTWARE
GLN C:99 , ARG C:105 , ASN C:137 , ARG C:168 , HIS C:192 , ALA C:237 , THR C:247 , NAI C:332
BINDING SITE FOR RESIDUE OXM C 333
09
AC9
SOFTWARE
ASN C:87 , SER C:88 , SER C:127 , PRO C:128 , HIS C:129
BINDING SITE FOR RESIDUE ACT C 334
10
BC1
SOFTWARE
LEU C:243
BINDING SITE FOR RESIDUE ACT C 335
11
BC2
SOFTWARE
GLY D:26 , GLY D:28 , ALA D:29 , VAL D:30 , ASP D:51 , VAL D:52 , MET D:53 , TYR D:82 , THR D:94 , ALA D:95 , PHE D:118 , ILE D:119 , VAL D:135 , SER D:136 , ASN D:137 , VAL D:139 , SER D:160 , HOH D:567 , HOH D:645 , HOH D:731
BINDING SITE FOR RESIDUE NAI D 332
12
BC3
SOFTWARE
ASN D:137 , ARG D:168 , HIS D:192 , ALA D:237
BINDING SITE FOR RESIDUE OXM D 333
13
BC4
SOFTWARE
LYS D:316
BINDING SITE FOR RESIDUE ACT D 334
14
BC5
SOFTWARE
GLY D:281 , GLU D:312
BINDING SITE FOR RESIDUE ACT D 335
15
BC6
SOFTWARE
LYS D:316 , ACT D:337
BINDING SITE FOR RESIDUE ACT D 336
16
BC7
SOFTWARE
SER D:309 , GLU D:312 , ALA D:313 , ACT D:336
BINDING SITE FOR RESIDUE ACT D 337
17
BC8
SOFTWARE
MET D:40 , ASP D:42 , PHE D:70
BINDING SITE FOR RESIDUE ACT D 338
18
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
19
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
20
CC2
SOFTWARE
LEU E:182 , HIS E:185 , HOH E:357 , HOH E:532 , ARG G:170
BINDING SITE FOR RESIDUE ACT E 334
21
CC3
SOFTWARE
ASP E:42 , PHE E:70
BINDING SITE FOR RESIDUE ACT E 335
22
CC4
SOFTWARE
ARG E:267 , HOH E:884
BINDING SITE FOR RESIDUE ACT E 336
23
CC5
SOFTWARE
LYS E:242
BINDING SITE FOR RESIDUE ACT E 337
24
CC6
SOFTWARE
ASP E:42 , ASP H:42 , ACT H:337
BINDING SITE FOR RESIDUE ACT E 338
25
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
26
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
27
CC9
SOFTWARE
MET F:40 , PHE F:70 , ARG F:72
BINDING SITE FOR RESIDUE ACT F 334
28
DC1
SOFTWARE
HIS F:16 , HOH F:1191
BINDING SITE FOR RESIDUE ACT F 335
29
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
30
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
31
DC4
SOFTWARE
ASP G:42 , PHE G:70 , LEU G:71 , ARG G:72
BINDING SITE FOR RESIDUE ACT G 334
32
DC5
SOFTWARE
LEU G:213 , HIS G:214 , PRO G:215 , LYS G:223 , GLN H:6
BINDING SITE FOR RESIDUE ACT G 335
33
DC6
SOFTWARE
LEU G:329 , GLN G:330 , PHE G:331
BINDING SITE FOR RESIDUE ACT G 336
34
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
35
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
36
DC9
SOFTWARE
VAL H:305 , HOH H:853
BINDING SITE FOR RESIDUE ACT H 334
37
EC1
SOFTWARE
MET H:40 , ASP H:42
BINDING SITE FOR RESIDUE ACT H 335
38
EC2
SOFTWARE
LYS H:4
BINDING SITE FOR RESIDUE ACT H 336
39
EC3
SOFTWARE
ACT E:338 , LYS H:41 , GLU H:260
BINDING SITE FOR RESIDUE ACT H 337
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: L_LDH (A:189-195,B:189-195,C:189-195,D: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
8
A:189-195
B:189-195
C:189-195
D:189-195
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
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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)
View:
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Classes
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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
:
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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Pfam Domains
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