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1LDN
Biol. Unit 2
Info
Asym.Unit (430 KB)
Biol.Unit 1 (213 KB)
Biol.Unit 2 (214 KB)
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(1)
Title
:
STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION
Authors
:
D. B. Wigley, S. J. Gamblin, J. P. Turkenburg, E. J. Dodson, K. Piontek, H. Muirhead, J. J. Holbrook
Date
:
19 Nov 91 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
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
:
Oxidoreductase(Choh(D)-Nad(A))
(Keyword Search:
[
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]
)
Reference
:
D. B. Wigley, S. J. Gamblin, J. P. Turkenburg, E. J. Dodson, K. Piontek, H. Muirhead, J. J. Holbrook
Structure Of A Ternary Complex Of An Allosteric Lactate Dehydrogenase From Bacillus Stearothermophilus At 2. 5 A Resolution.
J. Mol. Biol. V. 223 317 1992
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPa)
1b: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPb)
1c: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPc)
1d: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPd)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
2f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
2h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
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
FBP
2
Ligand/Ion
BETA-FRUCTOSE-1,6-DIPHOSPHATE
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
OXM
4
Ligand/Ion
OXAMIC ACID
[
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Sites
(10, 10)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: BC4 (SOFTWARE)
04: BC5 (SOFTWARE)
05: BC6 (SOFTWARE)
06: BC7 (SOFTWARE)
07: BC8 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
ARG E:171 , GLN E:183 , ASN E:184 , HIS E:186 , GLN G:183 , HIS G:186
BINDING SITE FOR RESIDUE FBP E 353
02
AC4
SOFTWARE
ARG F:171 , GLN F:183 , ASN F:184 , HIS F:186 , ARG H:171 , GLN H:183 , ASN H:184 , HIS H:186
BINDING SITE FOR RESIDUE FBP F 353
03
BC4
SOFTWARE
ARG E:106 , ASN E:138 , LEU E:165 , ARG E:169 , HIS E:193 , ALA E:237 , THR E:247 , NAD E:352 , HOH E:369
BINDING SITE FOR RESIDUE OXM E 351
04
BC5
SOFTWARE
ALA E:28 , GLY E:29 , PHE E:30 , VAL E:31 , ASP E:52 , ALA E:53 , CYS E:95 , ALA E:96 , GLY E:97 , ALA E:98 , ASN E:99 , ASN E:113 , ILE E:116 , ALA E:136 , THR E:137 , ASN E:138 , SER E:161 , LEU E:165 , HIS E:193 , THR E:247 , ILE E:251 , OXM E:351 , HOH E:363 , HOH E:367 , HOH E:381 , HOH E:407 , HOH E:408
BINDING SITE FOR RESIDUE NAD E 352
05
BC6
SOFTWARE
GLN F:100 , ARG F:106 , ASN F:138 , ARG F:169 , HIS F:193 , THR F:247 , NAD F:352
BINDING SITE FOR RESIDUE OXM F 351
06
BC7
SOFTWARE
GLY F:29 , PHE F:30 , VAL F:31 , ASP F:52 , ALA F:53 , CYS F:95 , GLY F:97 , ALA F:98 , ASN F:99 , ILE F:116 , ALA F:136 , THR F:137 , ASN F:138 , SER F:161 , HIS F:193 , THR F:247 , ILE F:251 , OXM F:351 , HOH F:359 , HOH F:365 , HOH F:369 , HOH F:371 , HOH F:383 , HOH F:408 , HOH F:409
BINDING SITE FOR RESIDUE NAD F 352
07
BC8
SOFTWARE
GLN G:100 , ARG G:106 , ASN G:138 , ARG G:169 , HIS G:193 , THR G:247 , NAD G:352
BINDING SITE FOR RESIDUE OXM G 351
08
BC9
SOFTWARE
GLY G:27 , ALA G:28 , GLY G:29 , PHE G:30 , VAL G:31 , ASP G:52 , ALA G:53 , CYS G:95 , ALA G:96 , GLY G:97 , ALA G:98 , ILE G:116 , ALA G:136 , THR G:137 , ASN G:138 , SER G:161 , HIS G:193 , THR G:247 , ILE G:251 , OXM G:351 , HOH G:434 , HOH G:450 , HOH G:452 , HOH G:464 , HOH G:491 , HOH G:492
BINDING SITE FOR RESIDUE NAD G 352
09
CC1
SOFTWARE
GLN H:100 , ARG H:106 , ASN H:138 , ARG H:169 , HIS H:193 , ALA H:237 , THR H:247 , NAD H:352 , HOH H:378
BINDING SITE FOR RESIDUE OXM H 351
10
CC2
SOFTWARE
ALA H:28 , GLY H:29 , PHE H:30 , VAL H:31 , ASP H:52 , ALA H:53 , CYS H:95 , ALA H:96 , GLY H:97 , ALA H:98 , ASN H:99 , ILE H:116 , ILE H:120 , ALA H:136 , THR H:137 , ASN H:138 , SER H:161 , HIS H:193 , THR H:247 , ILE H:251 , OXM H:351 , HOH H:365 , HOH H:377 , HOH H:379 , HOH H:416 , HOH H:417
BINDING SITE FOR RESIDUE NAD H 352
[
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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:190-196,F:190-196,G:190-196,H: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
-
-
-
-
E:190-196
F:190-196
G:190-196
H:190-196
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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_d1ldna2 (A:163-330)
1b: SCOP_d1ldnb2 (B:163-330)
1c: SCOP_d1ldnc2 (C:163-330)
1d: SCOP_d1ldnd2 (D:163-330)
1e: SCOP_d1ldne2 (E:163-330)
1f: SCOP_d1ldnf2 (F:163-330)
1g: SCOP_d1ldng2 (G:163-330)
1h: SCOP_d1ldnh2 (H:163-330)
2a: SCOP_d1ldna1 (A:15-162)
2b: SCOP_d1ldnb1 (B:15-162)
2c: SCOP_d1ldnc1 (C:15-162)
2d: SCOP_d1ldnd1 (D:15-162)
2e: SCOP_d1ldne1 (E:15-162)
2f: SCOP_d1ldnf1 (F:15-162)
2g: SCOP_d1ldng1 (G:15-162)
2h: SCOP_d1ldnh1 (H:15-162)
View:
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1ldna2
A:163-330
1b
d1ldnb2
B:163-330
1c
d1ldnc2
C:163-330
1d
d1ldnd2
D:163-330
1e
d1ldne2
E:163-330
1f
d1ldnf2
F:163-330
1g
d1ldng2
G:163-330
1h
d1ldnh2
H:163-330
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
d1ldna1
A:15-162
2b
d1ldnb1
B:15-162
2c
d1ldnc1
C:15-162
2d
d1ldnd1
D:15-162
2e
d1ldne1
E:15-162
2f
d1ldnf1
F:15-162
2g
d1ldng1
G:15-162
2h
d1ldnh1
H:15-162
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1ldnA01 (A:15-162)
1b: CATH_1ldnB01 (B:15-162)
1c: CATH_1ldnC01 (C:15-162)
1d: CATH_1ldnD01 (D:15-162)
1e: CATH_1ldnE01 (E:15-162)
1f: CATH_1ldnF01 (F:15-162)
1g: CATH_1ldnG01 (G:15-162)
1h: CATH_1ldnH01 (H:15-162)
2a: CATH_1ldnA02 (A:163-330)
2b: CATH_1ldnB02 (B:163-330)
2c: CATH_1ldnC02 (C:163-330)
2d: CATH_1ldnD02 (D:163-330)
2e: CATH_1ldnE02 (E:163-330)
2f: CATH_1ldnF02 (F:163-330)
2g: CATH_1ldnG02 (G:163-330)
2h: CATH_1ldnH02 (H:163-330)
View:
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)
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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
1ldnA01
A:15-162
1b
1ldnB01
B:15-162
1c
1ldnC01
C:15-162
1d
1ldnD01
D:15-162
1e
1ldnE01
E:15-162
1f
1ldnF01
F:15-162
1g
1ldnG01
G:15-162
1h
1ldnH01
H: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
1ldnA02
A:163-330
2b
1ldnB02
B:163-330
2c
1ldnC02
C:163-330
2d
1ldnD02
D:163-330
2e
1ldnE02
E:163-330
2f
1ldnF02
F:163-330
2g
1ldnG02
G:163-330
2h
1ldnH02
H:163-330
[
close CATH info
]
Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_Ldh_1_C_1ldnH01 (H:163-330)
1b: PFAM_Ldh_1_C_1ldnH02 (H:163-330)
1c: PFAM_Ldh_1_C_1ldnH03 (H:163-330)
1d: PFAM_Ldh_1_C_1ldnH04 (H:163-330)
1e: PFAM_Ldh_1_C_1ldnH05 (H:163-330)
1f: PFAM_Ldh_1_C_1ldnH06 (H:163-330)
1g: PFAM_Ldh_1_C_1ldnH07 (H:163-330)
1h: PFAM_Ldh_1_C_1ldnH08 (H:163-330)
2a: PFAM_Ldh_1_N_1ldnH09 (H:21-161)
2b: PFAM_Ldh_1_N_1ldnH10 (H:21-161)
2c: PFAM_Ldh_1_N_1ldnH11 (H:21-161)
2d: PFAM_Ldh_1_N_1ldnH12 (H:21-161)
2e: PFAM_Ldh_1_N_1ldnH13 (H:21-161)
2f: PFAM_Ldh_1_N_1ldnH14 (H:21-161)
2g: PFAM_Ldh_1_N_1ldnH15 (H:21-161)
2h: PFAM_Ldh_1_N_1ldnH16 (H:21-161)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LDH_C
(56)
Family
:
Ldh_1_C
(51)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(1)
1a
Ldh_1_C-1ldnH01
H:163-330
1b
Ldh_1_C-1ldnH02
H:163-330
1c
Ldh_1_C-1ldnH03
H:163-330
1d
Ldh_1_C-1ldnH04
H:163-330
1e
Ldh_1_C-1ldnH05
H:163-330
1f
Ldh_1_C-1ldnH06
H:163-330
1g
Ldh_1_C-1ldnH07
H:163-330
1h
Ldh_1_C-1ldnH08
H:163-330
Clan
:
NADP_Rossmann
(1239)
Family
:
Ldh_1_N
(51)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(1)
2a
Ldh_1_N-1ldnH09
H:21-161
2b
Ldh_1_N-1ldnH10
H:21-161
2c
Ldh_1_N-1ldnH11
H:21-161
2d
Ldh_1_N-1ldnH12
H:21-161
2e
Ldh_1_N-1ldnH13
H:21-161
2f
Ldh_1_N-1ldnH14
H:21-161
2g
Ldh_1_N-1ldnH15
H:21-161
2h
Ldh_1_N-1ldnH16
H:21-161
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Asym.Unit (430 KB)
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