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3PK0
Asym. Unit
Info
Asym.Unit (328 KB)
Biol.Unit 1 (322 KB)
Biol.Unit 2 (320 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE/REDUCTASE SDR FROM MYCOBACTERIUM SMEGMATIS
Authors
:
Seattle Structural Genomics Center For Infectious Disease (S
Date
:
10 Nov 10 (Deposition) - 24 Nov 10 (Release) - 22 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (2x)
Biol. Unit 2: B,D (2x)
Keywords
:
Ssgcid, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
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Hetero Components
(4, 18)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
2
CL
4
Ligand/Ion
CHLORIDE ION
3
GOL
7
Ligand/Ion
GLYCEROL
4
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:95 , TRP A:154 , HOH A:340 , HOH A:870
BINDING SITE FOR RESIDUE PEG A 265
02
AC2
SOFTWARE
ASP A:97 , HOH A:291 , HOH A:598 , ASP C:97 , HOH C:302
BINDING SITE FOR RESIDUE CA A 270
03
AC3
SOFTWARE
LEU A:165 , ARG A:169 , CL C:275
BINDING SITE FOR RESIDUE CL A 275
04
AC4
SOFTWARE
ASP A:51 , GLY A:54 , GLY A:56 , HOH A:283 , HOH A:319
BINDING SITE FOR RESIDUE CA A 280
05
AC5
SOFTWARE
ASN A:91 , GLY A:93 , THR A:141 , TYR A:157 , LYS A:161
BINDING SITE FOR RESIDUE GOL A 285
06
AC6
SOFTWARE
TYR B:151 , HOH B:341 , HOH B:467 , HOH B:879
BINDING SITE FOR RESIDUE GOL B 267
07
AC7
SOFTWARE
ASP B:97 , HOH B:291 , HOH B:331 , HOH B:772 , ASP D:97 , HOH D:327 , HOH D:658
BINDING SITE FOR RESIDUE CA B 270
08
AC8
SOFTWARE
ARG B:169 , CL D:275
BINDING SITE FOR RESIDUE CL B 275
09
AC9
SOFTWARE
ASP B:51 , GLY B:54 , GLY B:56 , HOH B:319 , HOH B:431
BINDING SITE FOR RESIDUE CA B 280
10
BC1
SOFTWARE
ASN B:91 , ALA B:92 , GLY B:93 , THR B:141 , TYR B:157 , LYS B:161 , HOH B:296
BINDING SITE FOR RESIDUE GOL B 285
11
BC2
SOFTWARE
HOH C:889
BINDING SITE FOR RESIDUE GOL C 267
12
BC3
SOFTWARE
CL A:275 , ARG C:169
BINDING SITE FOR RESIDUE CL C 275
13
BC4
SOFTWARE
ASP C:51 , GLY C:54 , GLY C:56 , HOH C:311 , HOH C:532
BINDING SITE FOR RESIDUE CA C 280
14
BC5
SOFTWARE
ASN C:91 , ALA C:92 , GLY C:93 , THR C:141 , TYR C:157 , LYS C:161 , HOH C:330
BINDING SITE FOR RESIDUE GOL C 285
15
BC6
SOFTWARE
HOH D:514 , HOH D:828 , HOH D:903
BINDING SITE FOR RESIDUE GOL D 267
16
BC7
SOFTWARE
CL B:275 , LEU D:165 , ARG D:169
BINDING SITE FOR RESIDUE CL D 275
17
BC8
SOFTWARE
PRO C:-2 , HOH C:509 , ASP D:51 , GLY D:54 , GLY D:56 , HOH D:315
BINDING SITE FOR RESIDUE CA D 280
18
BC9
SOFTWARE
ASN D:91 , ALA D:92 , GLY D:93 , THR D:141 , TYR D:157 , LYS D:161 , HOH D:344
BINDING SITE FOR RESIDUE GOL D 285
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3pk0a_ (A:)
1b: SCOP_d3pk0b_ (B:)
1c: SCOP_d3pk0c_ (C:)
1d: SCOP_d3pk0d_ (D:)
View:
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Classes
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Folds
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Mycobacterium smegmatis [TaxId: 246196]
(4)
1a
d3pk0a_
A:
1b
d3pk0b_
B:
1c
d3pk0c_
C:
1d
d3pk0d_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_adh_short_3pk0D01 (D:7-176)
1b: PFAM_adh_short_3pk0D02 (D:7-176)
1c: PFAM_adh_short_3pk0D03 (D:7-176)
1d: PFAM_adh_short_3pk0D04 (D:7-176)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
adh_short
(92)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
(2)
1a
adh_short-3pk0D01
D:7-176
1b
adh_short-3pk0D02
D:7-176
1c
adh_short-3pk0D03
D:7-176
1d
adh_short-3pk0D04
D:7-176
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Chain D
Asymmetric Unit 1
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Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (328 KB)
Header - Asym.Unit
Biol.Unit 1 (322 KB)
Header - Biol.Unit 1
Biol.Unit 2 (320 KB)
Header - Biol.Unit 2
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