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1YIW
Biol. Unit 6
Info
Asym.Unit (49 KB)
Biol.Unit 1 (16 KB)
Biol.Unit 2 (16 KB)
Biol.Unit 3 (16 KB)
Biol.Unit 4 (42 KB)
Biol.Unit 5 (42 KB)
Biol.Unit 6 (28 KB)
Biol.Unit 7 (29 KB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED UBIQUITIN
Authors
:
D. Bang, G. I. Makhatadze, V. Tereshko, A. A. Kossiakoff, S. B. Kent
Date
:
13 Jan 05 (Deposition) - 14 Jun 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.39
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: A,B,C (1x)
Biol. Unit 5: A,B,C (1x)
Biol. Unit 6: A,B (1x)
Biol. Unit 7: A,C (1x)
Keywords
:
Ubiquitin, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
D. Bang, G. I. Makhatadze, V. Tereshko, A. A. Kossiakoff, S. B. Kent
X-Ray Crystal Structure Of A Chemically Synthesized [D-Gln35]Ubiquitin
Angew. Chem. Int. Ed. Engl. V. 44 3852 2005
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Hetero Components
(0, 0)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
1e: CADMIUM ION (CDe)
1f: CADMIUM ION (CDf)
1g: CADMIUM ION (CDg)
1h: CADMIUM ION (CDh)
1i: CADMIUM ION (CDi)
1j: CADMIUM ION (CDj)
1k: CADMIUM ION (CDk)
1l: CADMIUM ION (CDl)
1m: CADMIUM ION (CDm)
1n: CADMIUM ION (CDn)
1o: CADMIUM ION (CDo)
1p: CADMIUM ION (CDp)
1q: CADMIUM ION (CDq)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
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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: BC9 (SOFTWARE)
18: CC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CL A:92 , HOH A:95 , CL B:93 , HOH B:96 , CL C:91 , HOH C:94
BINDING SITE FOR RESIDUE CD A 90
02
AC2
SOFTWARE
SER A:20 , ASP A:21 , CD A:90 , ASN C:25
BINDING SITE FOR RESIDUE CL C 91
03
AC3
SOFTWARE
ASN A:25 , CD A:90 , SER B:20
BINDING SITE FOR RESIDUE CL A 92
04
AC4
SOFTWARE
CD A:90 , ASN B:25 , SER C:20 , ASP C:21
BINDING SITE FOR RESIDUE CL B 93
05
AC5
SOFTWARE
ASP A:21 , HOH A:102 , HOH A:103 , GLU B:18
BINDING SITE FOR RESIDUE CD A 101
06
AC6
SOFTWARE
GLU A:24 , ASP A:52 , HOH A:105 , HOH A:106 , HOH A:107
BINDING SITE FOR RESIDUE CD A 104
07
AC7
SOFTWARE
HIS A:68 , HOH A:109 , HOH A:110 , HOH A:111 , HOH A:112 , HOH A:113
BINDING SITE FOR RESIDUE CD A 108
08
AC8
SOFTWARE
ASP A:58 , HOH A:115 , HOH A:116 , HOH A:117 , HOH A:118
BINDING SITE FOR RESIDUE CD A 114
09
AC9
SOFTWARE
HIS A:68 , HOH A:120 , HOH A:122 , HOH A:123 , HOH A:124
BINDING SITE FOR RESIDUE CD A 119
10
BC1
SOFTWARE
ASP B:21 , HOH B:202 , HOH B:203 , GLU C:18
BINDING SITE FOR RESIDUE CD B 201
11
BC2
SOFTWARE
GLU B:24 , ASP B:52 , HOH B:205 , HOH B:206 , HOH B:207
BINDING SITE FOR RESIDUE CD B 204
12
BC3
SOFTWARE
HIS B:68 , HOH B:209 , HOH B:210 , HOH B:211 , HOH B:212 , HOH B:213
BINDING SITE FOR RESIDUE CD B 208
13
BC4
SOFTWARE
ASP B:58 , HOH B:215 , HOH B:216 , HOH B:217 , HOH B:218
BINDING SITE FOR RESIDUE CD B 214
14
BC5
SOFTWARE
GLU B:64 , HOH C:226 , HOH C:228
BINDING SITE FOR RESIDUE CD B 225
15
BC6
SOFTWARE
ASP B:39 , GLN B:40
BINDING SITE FOR RESIDUE CD B 229
16
BC7
SOFTWARE
GLU A:18 , ASP C:21 , HOH C:302 , HOH C:303
BINDING SITE FOR RESIDUE CD A 301
17
BC9
SOFTWARE
ASP A:39 , HIS C:68 , HOH C:309 , HOH C:310 , HOH C:311
BINDING SITE FOR RESIDUE CD C 308
18
CC2
SOFTWARE
HOH A:327 , GLU C:64 , HOH C:326
BINDING SITE FOR RESIDUE CD C 325
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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All Exons
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All Exon Boundaries
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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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1yiwa1 (A:1-71)
1b: SCOP_d1yiwb1 (B:1-71)
1c: SCOP_d1yiwc1 (C:1-71)
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Classes
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(
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Folds
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Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Designed proteins
(167)
Fold
:
Ubiquitin
(6)
Superfamily
:
Ubiquitin
(6)
Family
:
Ubiquitin
(6)
Protein domain
:
Ubiquitin
(6)
Synthetic
(6)
1a
d1yiwa1
A:1-71
1b
d1yiwb1
B:1-71
1c
d1yiwc1
C:1-71
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1yiwC00 (C:1-74)
1b: CATH_1yiwB00 (B:1-71)
1c: CATH_1yiwA00 (A:1-71)
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Organisms
(
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(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
(286)
[unclassified]
(11)
1a
1yiwC00
C:1-74
1b
1yiwB00
B:1-71
1c
1yiwA00
A:1-71
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (49 KB)
Header - Asym.Unit
Biol.Unit 1 (16 KB)
Header - Biol.Unit 1
Biol.Unit 2 (16 KB)
Header - Biol.Unit 2
Biol.Unit 3 (16 KB)
Header - Biol.Unit 3
Biol.Unit 4 (42 KB)
Header - Biol.Unit 4
Biol.Unit 5 (42 KB)
Header - Biol.Unit 5
Biol.Unit 6 (28 KB)
Header - Biol.Unit 6
Biol.Unit 7 (29 KB)
Header - Biol.Unit 7
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