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1PB0
Asym. Unit
Info
Asym.Unit (131 KB)
Biol.Unit 1 (125 KB)
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(1)
Title
:
YCDX PROTEIN IN AUTOINHIBITED STATE
Authors
:
A. Teplyakov, G. Obmolova, P. P. Khil, R. D. Camerini-Otero, G. L. Gilliland
Date
:
14 May 03 (Deposition) - 25 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Structural Genomics, Beta-Alpha-Barrel, Trinuclear Zinc, Autoinhibition, Unknown Function
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Teplyakov, G. Obmolova, P. P. Khil, R. D. Camerini-Otero, G. L. Gilliland
Autoregulation Of Ycdx Protein
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 19)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
1b: FORMIC ACID (FMTb)
1c: FORMIC ACID (FMTc)
1d: FORMIC ACID (FMTd)
1e: FORMIC ACID (FMTe)
1f: FORMIC ACID (FMTf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
3i: ZINC ION (ZNi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
6
Ligand/Ion
FORMIC ACID
2
SO4
4
Ligand/Ion
SULFATE ION
3
ZN
9
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:15 , HIS A:40 , HIS A:164 , HIS A:194
BINDING SITE FOR RESIDUE ZN A 1301
02
AC2
SOFTWARE
HIS A:7 , HIS A:9 , GLU A:73 , ASP A:192 , ZN A:1303 , HOH A:1334
BINDING SITE FOR RESIDUE ZN A 1302
03
AC3
SOFTWARE
GLU A:73 , HIS A:101 , HIS A:131 , ZN A:1302 , HOH A:1334
BINDING SITE FOR RESIDUE ZN A 1303
04
AC4
SOFTWARE
HIS B:15 , HIS B:40 , HIS B:164 , HIS B:194
BINDING SITE FOR RESIDUE ZN B 1311
05
AC5
SOFTWARE
HIS B:7 , HIS B:9 , GLU B:73 , ASP B:192 , ZN B:1313 , HOH B:1399
BINDING SITE FOR RESIDUE ZN B 1312
06
AC6
SOFTWARE
GLU B:73 , HIS B:101 , HIS B:131 , ZN B:1312 , HOH B:1399
BINDING SITE FOR RESIDUE ZN B 1313
07
AC7
SOFTWARE
HIS C:15 , HIS C:40 , HIS C:164 , HIS C:194
BINDING SITE FOR RESIDUE ZN C 1321
08
AC8
SOFTWARE
HIS C:7 , HIS C:9 , GLU C:73 , ASP C:192 , ZN C:1323 , HOH C:1354
BINDING SITE FOR RESIDUE ZN C 1322
09
AC9
SOFTWARE
GLU C:73 , HIS C:101 , HIS C:131 , ZN C:1322 , HOH C:1354
BINDING SITE FOR RESIDUE ZN C 1323
10
BC1
SOFTWARE
GLN A:152 , TRP A:186 , ARG A:218 , HOH A:1348 , HOH A:1439 , HOH A:1532
BINDING SITE FOR RESIDUE SO4 A 1324
11
BC2
SOFTWARE
GLN B:152 , TRP B:186 , ARG B:218 , HOH B:1341 , HOH B:1452 , HOH B:1456
BINDING SITE FOR RESIDUE SO4 B 1334
12
BC3
SOFTWARE
GLN C:152 , TRP C:186 , ARG C:218 , HOH C:1348 , HOH C:1412 , HOH C:1465 , HOH C:1471
BINDING SITE FOR RESIDUE SO4 C 1344
13
BC4
SOFTWARE
ARG A:70 , HOH A:1376 , HOH A:1416 , HOH A:1504
BINDING SITE FOR RESIDUE SO4 A 1305
14
BC5
SOFTWARE
ARG A:61 , VAL A:62 , HOH A:1502
BINDING SITE FOR RESIDUE FMT A 1306
15
BC6
SOFTWARE
PRO B:60 , ARG B:61 , VAL B:62 , HOH B:1391
BINDING SITE FOR RESIDUE FMT B 1326
16
BC7
SOFTWARE
PRO C:60 , ARG C:61 , VAL C:62 , HOH C:1433 , HOH C:1595
BINDING SITE FOR RESIDUE FMT C 1336
17
BC8
SOFTWARE
ARG B:181 , VAL B:212
BINDING SITE FOR RESIDUE FMT B 1307
18
BC9
SOFTWARE
ARG C:181 , HOH C:1540
BINDING SITE FOR RESIDUE FMT C 1317
19
CC1
SOFTWARE
ARG B:70 , HOH B:1453 , HOH B:1492
BINDING SITE FOR RESIDUE FMT B 1318
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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, 3)
Info
All SCOP Domains
1a: SCOP_d1pb0a_ (A:)
1b: SCOP_d1pb0b_ (B:)
1c: SCOP_d1pb0c_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
7-stranded beta/alpha barrel
(137)
Superfamily
:
PHP domain-like
(6)
Family
:
PHP domain
(4)
Protein domain
:
Hypothetical protein YcdX
(3)
Escherichia coli [TaxId: 562]
(3)
1a
d1pb0a_
A:
1b
d1pb0b_
B:
1c
d1pb0c_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1pb0A00 (A:1-245)
1b: CATH_1pb0B00 (B:1-245)
1c: CATH_1pb0C00 (C:1-245)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Escherichia coli. Organism_taxid: 562.
(27)
1a
1pb0A00
A:1-245
1b
1pb0B00
B:1-245
1c
1pb0C00
C:1-245
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_PHP_1pb0C01 (C:4-175)
1b: PFAM_PHP_1pb0C02 (C:4-175)
1c: PFAM_PHP_1pb0C03 (C:4-175)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Amidohydrolase
(126)
Family
:
PHP
(10)
Escherichia coli (strain K12)
(2)
1a
PHP-1pb0C01
C:4-175
1b
PHP-1pb0C02
C:4-175
1c
PHP-1pb0C03
C:4-175
[
close Pfam info
]
Atom Selection
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all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
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by Nucleotide
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Miscellaneous
Script
Example Commands
Example Command
Action
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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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (131 KB)
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