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1YJ1
Asym. Unit
Info
Asym.Unit (51 KB)
Biol.Unit 1 (16 KB)
Biol.Unit 2 (16 KB)
Biol.Unit 3 (17 KB)
Biol.Unit 4 (43 KB)
Biol.Unit 5 (43 KB)
Biol.Unit 6 (29 KB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED [D-GLN35]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
:
1.30
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)
Keywords
:
Ubiquitin, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
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
(3, 23)
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)
3a: D-GLUTAMINE (DGNa)
3b: D-GLUTAMINE (DGNb)
3c: D-GLUTAMINE (DGNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
17
Ligand/Ion
CADMIUM ION
2
CL
3
Ligand/Ion
CHLORIDE ION
3
DGN
3
Mod. Amino Acid
D-GLUTAMINE
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Sites
(20, 20)
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)
20: CC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CL A:91 , CL A:92 , HOH A:95 , CL B:93 , HOH C:96 , HOH C:1341
BINDING SITE FOR RESIDUE CD A 90
02
AC2
SOFTWARE
SER A:20 , ASP A:21 , CD A:90 , ASN C:25 , HOH C:1341
BINDING SITE FOR RESIDUE CL A 91
03
AC3
SOFTWARE
ASN A:25 , CD A:90 , SER B:20 , ASP B:21 , HOH B:203
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 C:118
BINDING SITE FOR RESIDUE CD A 114
09
AC9
SOFTWARE
HOH A:120 , HOH A:121 , HOH A:122 , HOH A:123 , HOH A:124 , HOH B:1234
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 C:217 , HOH C:218
BINDING SITE FOR RESIDUE CD B 214
14
BC5
SOFTWARE
GLU B:64 , HOH B:227 , HOH B:228 , HOH C:1334
BINDING SITE FOR RESIDUE CD B 225
15
BC6
SOFTWARE
ASP B:39 , HOH B:230 , HOH B:231
BINDING SITE FOR RESIDUE CD B 229
16
BC7
SOFTWARE
GLU A:18 , HOH A:303 , ASP C:21 , HOH C:302
BINDING SITE FOR RESIDUE CD A 301
17
BC8
SOFTWARE
GLU C:24 , ASP C:52 , HOH C:305 , HOH C:306 , HOH C:307
BINDING SITE FOR RESIDUE CD C 304
18
BC9
SOFTWARE
ASP A:39 , HIS C:68 , HOH C:309 , HOH C:310 , HOH C:311
BINDING SITE FOR RESIDUE CD C 308
19
CC1
SOFTWARE
ASP C:58 , HOH C:315 , HOH C:316 , HOH C:317 , HOH C:318
BINDING SITE FOR RESIDUE CD C 314
20
CC2
SOFTWARE
GLU C:64 , HOH C:1346
BINDING SITE FOR RESIDUE CD C 325
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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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, 3)
Info
All SCOP Domains
1a: SCOP_d1yj1a1 (A:1-71)
1b: SCOP_d1yj1b1 (B:1-71)
1c: SCOP_d1yj1c1 (C:1-71)
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Protein Domains
(
)
(
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Organisms
(
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(
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Class
:
Designed proteins
(167)
Fold
:
Ubiquitin
(6)
Superfamily
:
Ubiquitin
(6)
Family
:
Ubiquitin
(6)
Protein domain
:
Ubiquitin
(6)
Synthetic
(6)
1a
d1yj1a1
A:1-71
1b
d1yj1b1
B:1-71
1c
d1yj1c1
C:1-71
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1yj1C00 (C:1-74)
1b: CATH_1yj1B00 (B:1-72)
1c: CATH_1yj1A00 (A:1-71)
View:
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Homologous Superfamilies
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Organisms
(
)
(
)
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
1yj1C00
C:1-74
1b
1yj1B00
B:1-72
1c
1yj1A00
A:1-71
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
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Miscellaneous
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Example Commands
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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Asym.Unit (51 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 (17 KB)
Header - Biol.Unit 3
Biol.Unit 4 (43 KB)
Header - Biol.Unit 4
Biol.Unit 5 (43 KB)
Header - Biol.Unit 5
Biol.Unit 6 (29 KB)
Header - Biol.Unit 6
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