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1IB6
Asym. Unit
Info
Asym.Unit (199 KB)
Biol.Unit 1 (99 KB)
Biol.Unit 2 (99 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF R153C E. COLI MALATE DEHYDROGENASE
Authors
:
J. K. Bell, H. P. Yennawar, S. K. Wright, J. R. Thompson, R. E. Viola, L. J. Banaszak
Date
:
27 Mar 01 (Deposition) - 19 Sep 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Oxidoreductase, Dehydrogenase, Malate Dehydrogenase, Substrate Specificity
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. K. Bell, H. P. Yennawar, S. K. Wright, J. R. Thompson, R. E. Viola, L. J. Banaszak
Structural Analyses Of A Malate Dehydrogenase With A Variable Active Site
J. Biol. Chem. V. 276 31156 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 9)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
3
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:81 , ARG A:87 , ASN A:119 , HIS A:177 , GLY A:210 , NAD A:313 , HOH A:344 , HOH A:353
BINDING SITE FOR RESIDUE SO4 A 316
2
AC2
SOFTWARE
ARG A:81 , ASP A:86 , ARG A:87 , SER A:88 , SER A:178 , GLY A:179
BINDING SITE FOR RESIDUE SO4 A 317
3
AC3
SOFTWARE
ARG C:81 , ARG C:87 , ASN C:119 , HIS C:177 , GLY C:210 , NAD C:314 , HOH C:473
BINDING SITE FOR RESIDUE SO4 C 318
4
AC4
SOFTWARE
ARG C:81 , ASP C:86 , ARG C:87 , SER C:88 , SER C:178 , GLY C:179 , HOH C:467
BINDING SITE FOR RESIDUE SO4 C 319
5
AC5
SOFTWARE
ARG D:81 , ARG D:87 , ASN D:119 , HIS D:177 , GLY D:210 , NAD D:315 , HOH D:531 , HOH D:532 , HOH D:533
BINDING SITE FOR RESIDUE SO4 D 320
6
AC6
SOFTWARE
ASP D:86 , ARG D:87 , SER D:88 , SER D:178 , GLY D:179
BINDING SITE FOR RESIDUE SO4 D 321
7
AC7
SOFTWARE
GLY A:7 , ALA A:9 , GLY A:10 , GLY A:11 , ILE A:12 , TYR A:33 , ASP A:34 , ILE A:35 , SER A:76 , ALA A:77 , GLY A:78 , VAL A:79 , ALA A:80 , LEU A:90 , ASN A:94 , ILE A:97 , ILE A:117 , THR A:118 , ASN A:119 , VAL A:146 , LEU A:149 , HIS A:177 , ALA A:223 , MET A:227 , SO4 A:316 , HOH A:343 , HOH A:345 , HOH A:348 , HOH A:349 , HOH A:396 , HOH A:397
BINDING SITE FOR RESIDUE NAD A 313
8
AC8
SOFTWARE
ALA C:9 , GLY C:10 , GLY C:11 , ILE C:12 , TYR C:33 , ASP C:34 , ILE C:35 , SER C:76 , ALA C:77 , GLY C:78 , VAL C:79 , ALA C:80 , ASN C:94 , ILE C:97 , ILE C:117 , ASN C:119 , VAL C:121 , VAL C:146 , HIS C:177 , ALA C:223 , THR C:224 , MET C:227 , SO4 C:318 , HOH C:473 , HOH C:474 , HOH C:475 , HOH C:479 , HOH C:480
BINDING SITE FOR RESIDUE NAD C 314
9
AC9
SOFTWARE
GLY D:7 , ALA D:9 , GLY D:10 , GLY D:11 , ILE D:12 , TYR D:33 , ASP D:34 , SER D:76 , ALA D:77 , GLY D:78 , VAL D:79 , LEU D:90 , ASN D:94 , ILE D:97 , ILE D:117 , ASN D:119 , VAL D:121 , VAL D:146 , HIS D:177 , ALA D:223 , THR D:224 , MET D:227 , SO4 D:320 , HOH D:529 , HOH D:530 , HOH D:531 , HOH D:549 , HOH D:563 , HOH D:564 , HOH D:577
BINDING SITE FOR RESIDUE NAD D 315
[
close Site info
]
SAPs(SNPs)/Variants
(11, 44)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_MDH_ECOLI_001 (D71N, chain A/B/C/D, )
02: VAR_MDH_ECOLI_002 (A106S, chain A/B/C/D, )
03: VAR_MDH_ECOLI_003 (A209P, chain A/B/C/D, )
04: VAR_MDH_ECOLI_004 (A218R, chain A/B/C/D, )
05: VAR_MDH_ECOLI_005 (A232T, chain A/B/C/D, )
06: VAR_MDH_ECOLI_006 (V249I, chain A/B/C/D, )
07: VAR_MDH_ECOLI_007 (Q289K, chain A/B/C/D, )
08: VAR_MDH_ECOLI_008 (N290S, chain A/B/C/D, )
09: VAR_MDH_ECOLI_009 (A291S, chain A/B/C/D, )
10: VAR_MDH_ECOLI_010 (G294A, chain A/B/C/D, )
11: VAR_MDH_ECOLI_011 (D297N, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_MDH_ECOLI_001
*
D
71
N
MDH_ECOLI
---
---
A/B/C/D
D
71
N
02
UniProt
VAR_MDH_ECOLI_002
*
A
106
S
MDH_ECOLI
---
---
A/B/C/D
A
106
S
03
UniProt
VAR_MDH_ECOLI_003
*
A
209
P
MDH_ECOLI
---
---
A/B/C/D
A
209
P
04
UniProt
VAR_MDH_ECOLI_004
*
A
218
R
MDH_ECOLI
---
---
A/B/C/D
A
218
R
05
UniProt
VAR_MDH_ECOLI_005
*
A
232
T
MDH_ECOLI
---
---
A/B/C/D
A
232
T
06
UniProt
VAR_MDH_ECOLI_006
*
V
249
I
MDH_ECOLI
---
---
A/B/C/D
V
249
I
07
UniProt
VAR_MDH_ECOLI_007
*
Q
289
K
MDH_ECOLI
---
---
A/B/C/D
Q
289
K
08
UniProt
VAR_MDH_ECOLI_008
*
N
290
S
MDH_ECOLI
---
---
A/B/C/D
N
290
S
09
UniProt
VAR_MDH_ECOLI_009
*
A
291
S
MDH_ECOLI
---
---
A/B/C/D
A
291
S
10
UniProt
VAR_MDH_ECOLI_010
*
G
294
A
MDH_ECOLI
---
---
A/B/C/D
G
294
A
11
UniProt
VAR_MDH_ECOLI_011
*
D
297
N
MDH_ECOLI
---
---
A/B/C/D
D
297
N
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: MDH (A:146-158,B:146-158,C:146-158,D:14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MDH
PS00068
Malate dehydrogenase active site signature.
MDH_ECOLI
146-158
4
A:146-158
B:146-158
C:146-158
D:146-158
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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_d1ib6a2 (A:146-312)
1b: SCOP_d1ib6b2 (B:146-312)
1c: SCOP_d1ib6c2 (C:146-312)
1d: SCOP_d1ib6d2 (D:146-312)
2a: SCOP_d1ib6a1 (A:1-145)
2b: SCOP_d1ib6b1 (B:1-145)
2c: SCOP_d1ib6c1 (C:1-145)
2d: SCOP_d1ib6d1 (D:1-145)
View:
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(
)
(
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(
)
(
)
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(
)
(
)
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
:
Malate dehydrogenase
(37)
Escherichia coli [TaxId: 562]
(4)
1a
d1ib6a2
A:146-312
1b
d1ib6b2
B:146-312
1c
d1ib6c2
C:146-312
1d
d1ib6d2
D:146-312
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
:
Malate dehydrogenase
(39)
Escherichia coli [TaxId: 562]
(4)
2a
d1ib6a1
A:1-145
2b
d1ib6b1
B:1-145
2c
d1ib6c1
C:1-145
2d
d1ib6d1
D:1-145
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ib6A01 (A:1-146)
1b: CATH_1ib6B01 (B:1-146)
1c: CATH_1ib6C01 (C:1-146)
1d: CATH_1ib6D01 (D:1-146)
2a: CATH_1ib6A02 (A:147-312)
2b: CATH_1ib6B02 (B:147-312)
2c: CATH_1ib6C02 (C:147-312)
2d: CATH_1ib6D02 (D:147-312)
View:
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(
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(
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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)
Escherichia coli. Organism_taxid: 562.
(48)
1a
1ib6A01
A:1-146
1b
1ib6B01
B:1-146
1c
1ib6C01
C:1-146
1d
1ib6D01
D:1-146
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)
Escherichia coli. Organism_taxid: 562.
(2)
2a
1ib6A02
A:147-312
2b
1ib6B02
B:147-312
2c
1ib6C02
C:147-312
2d
1ib6D02
D:147-312
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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