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Asym. Unit
Info
Asym.Unit (197 KB)
Biol.Unit 1 (191 KB)
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(1)
Title
:
STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE
Authors
:
K. Piontek, M. G. Rossmann
Date
:
27 Mar 89 (Deposition) - 12 Jul 89 (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
:
Oxidoreductase(Choh(D)-Nad(A))
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Piontek, P. Chakrabarti, H. P. Schar, M. G. Rossmann, H. Zuber
Structure Determination And Refinement Of Bacillus Stearothermophilus Lactate Dehydrogenase.
Proteins V. 7 74 1990
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPa)
1b: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPb)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FBP
2
Ligand/Ion
BETA-FRUCTOSE-1,6-DIPHOSPHATE
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
SO4
8
Ligand/Ion
SULFATE ION
[
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Sites
(22, 22)
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: FBA (AUTHOR)
16: FBB (AUTHOR)
17: FBC (AUTHOR)
18: FBD (AUTHOR)
19: NAA (AUTHOR)
20: NAB (AUTHOR)
21: NAC (AUTHOR)
22: NAD (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:183 , HIS A:186 , ARG D:171 , GLN D:183 , HIS D:186
BINDING SITE FOR RESIDUE FBP D 2
02
AC2
SOFTWARE
GLN B:183 , HIS B:186 , ARG C:171 , GLN C:183 , HIS C:186
BINDING SITE FOR RESIDUE FBP C 6
03
AC3
SOFTWARE
NAD A:1 , LEU A:165 , ARG A:169 , HIS A:193 , ALA A:237 , THR A:247
BINDING SITE FOR RESIDUE SO4 A 3
04
AC4
SOFTWARE
GLY A:43 , ALA A:45 , ASP A:46 , PRO A:73 , LYS A:74 , HOH A:371 , HIS B:264
BINDING SITE FOR RESIDUE SO4 A 4
05
AC5
SOFTWARE
NAD B:5 , LEU B:165 , ARG B:169 , HIS B:193 , ALA B:237 , THR B:247
BINDING SITE FOR RESIDUE SO4 B 7
06
AC6
SOFTWARE
HIS A:264 , GLY B:43 , ALA B:45 , ASP B:46 , PRO B:73 , LYS B:74
BINDING SITE FOR RESIDUE SO4 B 8
07
AC7
SOFTWARE
NAD C:9 , LEU C:165 , ARG C:169 , HIS C:193 , ALA C:237 , THR C:247
BINDING SITE FOR RESIDUE SO4 C 11
08
AC8
SOFTWARE
GLY C:43 , ALA C:45 , ASP C:46 , PRO C:73 , LYS C:74 , HIS D:264
BINDING SITE FOR RESIDUE SO4 C 12
09
AC9
SOFTWARE
NAD D:13 , LEU D:165 , ARG D:169 , HIS D:193 , ALA D:237 , THR D:247
BINDING SITE FOR RESIDUE SO4 D 332
10
BC1
SOFTWARE
HIS C:264 , GLY D:43 , ALA D:45 , ASP D:46 , PRO D:73 , LYS D:74
BINDING SITE FOR RESIDUE SO4 D 333
11
BC2
SOFTWARE
SO4 A:3 , ALA A:28 , GLY A:29 , PHE A:30 , VAL A:31 , ASP A:52 , ALA A:53 , ASN A:54 , CYS A:95 , ALA A:96 , GLY A:97 , ILE A:116 , ALA A:136 , THR A:137 , ASN A:138 , SER A:161 , LEU A:165 , HIS A:193 , ILE A:251 , HOH A:352
BINDING SITE FOR RESIDUE NAD A 1
12
BC3
SOFTWARE
SO4 B:7 , ALA B:28 , GLY B:29 , PHE B:30 , VAL B:31 , ASP B:52 , ALA B:53 , ASN B:54 , CYS B:95 , ALA B:96 , GLY B:97 , ILE B:116 , ALA B:136 , THR B:137 , ASN B:138 , SER B:161 , LEU B:165 , HIS B:193 , ILE B:251
BINDING SITE FOR RESIDUE NAD B 5
13
BC4
SOFTWARE
SO4 C:11 , ALA C:28 , GLY C:29 , PHE C:30 , VAL C:31 , ASP C:52 , ALA C:53 , ASN C:54 , CYS C:95 , ALA C:96 , GLY C:97 , ILE C:116 , ALA C:136 , THR C:137 , ASN C:138 , SER C:161 , LEU C:165 , HIS C:193 , ILE C:251
BINDING SITE FOR RESIDUE NAD C 9
14
BC5
SOFTWARE
ALA D:28 , GLY D:29 , PHE D:30 , VAL D:31 , ASP D:52 , ALA D:53 , ASN D:54 , CYS D:95 , ALA D:96 , GLY D:97 , ILE D:116 , ALA D:136 , THR D:137 , ASN D:138 , SER D:161 , LEU D:165 , HIS D:193 , ILE D:251 , SO4 D:332
BINDING SITE FOR RESIDUE NAD D 13
15
FBA
AUTHOR
ARG A:171 , PRO A:182 , GLN A:183 , ASN A:184 , VAL A:185 , HIS A:186 , ALA A:187 , TYR A:188 , GLY A:207 , ILE A:269
FBP BINDING SITE
16
FBB
AUTHOR
ARG B:171 , PRO B:182 , GLN B:183 , ASN B:184 , VAL B:185 , HIS B:186 , ALA B:187 , TYR B:188 , GLY B:207 , ILE B:269
FBP BINDING SITE
17
FBC
AUTHOR
ARG C:171 , PRO C:182 , GLN C:183 , ASN C:184 , VAL C:185 , HIS C:186 , ALA C:187 , TYR C:188 , GLY C:207 , ILE C:269
FBP BINDING SITE
18
FBD
AUTHOR
ARG D:171 , PRO D:182 , GLN D:183 , ASN D:184 , VAL D:185 , HIS D:186 , ALA D:187 , TYR D:188 , GLY D:207 , ILE D:269
FBP BINDING SITE
19
NAA
AUTHOR
ILE A:26 , GLY A:27 , ALA A:28 , GLY A:29 , PHE A:30 , VAL A:31 , GLY A:32 , ILE A:51 , ASP A:52 , ALA A:53 , ASN A:54 , LYS A:57 , TYR A:83 , CYS A:95 , ALA A:96 , GLY A:97 , ALA A:98 , ILE A:116 , ILE A:120 , ALA A:136 , THR A:137 , ASN A:138 , SER A:161 , LEU A:165 , HIS A:193
NAD BINDING SITE
20
NAB
AUTHOR
ILE B:26 , GLY B:27 , ALA B:28 , GLY B:29 , PHE B:30 , VAL B:31 , GLY B:32 , ILE B:51 , ASP B:52 , ALA B:53 , ASN B:54 , LYS B:57 , TYR B:83 , CYS B:95 , ALA B:96 , GLY B:97 , ALA B:98 , ILE B:116 , ILE B:120 , ALA B:136 , THR B:137 , ASN B:138 , SER B:161 , LEU B:165 , HIS B:193
NAD BINDING SITE
21
NAC
AUTHOR
ILE C:26 , GLY C:27 , ALA C:28 , GLY C:29 , PHE C:30 , VAL C:31 , GLY C:32 , ILE C:51 , ASP C:52 , ALA C:53 , ASN C:54 , LYS C:57 , TYR C:83 , CYS C:95 , ALA C:96 , GLY C:97 , ALA C:98 , ILE C:116 , ILE C:120 , ALA C:136 , THR C:137 , ASN C:138 , SER C:161 , LEU C:165 , HIS C:193
NAD BINDING SITE
22
NAD
AUTHOR
ILE D:26 , GLY D:27 , ALA D:28 , GLY D:29 , PHE D:30 , VAL D:31 , GLY D:32 , ILE D:51 , ASP D:52 , ALA D:53 , ASN D:54 , LYS D:57 , TYR D:83 , CYS D:95 , ALA D:96 , GLY D:97 , ALA D:98 , ILE D:116 , ILE D:120 , ALA D:136 , THR D:137 , ASN D:138 , SER D:161 , LEU D:165 , HIS D:193
NAD BINDING SITE
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
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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:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
L_LDH
PS00064
L-lactate dehydrogenase active site.
LDH_GEOSE
176-182
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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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2ldba2 (A:163-331)
1b: SCOP_d2ldbc2 (C:163-331)
1c: SCOP_d2ldbd2 (D:163-331)
1d: SCOP_d2ldbb2 (B:163-331)
2a: SCOP_d2ldba1 (A:15-162)
2b: SCOP_d2ldbc1 (C:15-162)
2c: SCOP_d2ldbd1 (D:15-162)
2d: SCOP_d2ldbb1 (B:15-162)
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)
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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)
Bacillus stearothermophilus [TaxId: 1422]
(3)
1a
d2ldba2
A:163-331
1b
d2ldbc2
C:163-331
1c
d2ldbd2
D:163-331
1d
d2ldbb2
B:163-331
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
:
Lactate dehydrogenase
(53)
Bacillus stearothermophilus [TaxId: 1422]
(3)
2a
d2ldba1
A:15-162
2b
d2ldbc1
C:15-162
2c
d2ldbd1
D:15-162
2d
d2ldbb1
B:15-162
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2ldbA01 (A:15-162)
1b: CATH_2ldbB01 (B:15-162)
1c: CATH_2ldbC01 (C:15-162)
1d: CATH_2ldbD01 (D:15-162)
2a: CATH_2ldbA02 (A:163-328)
2b: CATH_2ldbB02 (B:163-328)
2c: CATH_2ldbC02 (C:163-328)
2d: CATH_2ldbD02 (D:163-328)
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Geobacillus stearothermophilus. Organism_taxid: 1422
(3)
1a
2ldbA01
A:15-162
1b
2ldbB01
B:15-162
1c
2ldbC01
C:15-162
1d
2ldbD01
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)
Geobacillus stearothermophilus. Organism_taxid: 1422
(3)
2a
2ldbA02
A:163-328
2b
2ldbB02
B:163-328
2c
2ldbC02
C:163-328
2d
2ldbD02
D:163-328
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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