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1Z2U
Asym. Unit
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Asym.Unit (62 KB)
Biol.Unit 1 (57 KB)
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(1)
Title
:
THE 1.1A CRYSTALLOGRAPHIC STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME (UBC-2) FROM CAENORHABDITIS ELEGANS: FUNCTIONAL AND EVOLUTIONARY SIGNIFICANCE
Authors
:
J. A. Gavira, E. Digiamamarino, W. Tempel, Z. J. Liu, B. C. Wang, E. Meehan, J. D. Ng, Southeast Collaboratory For Structural Genomics (Secsg)
Date
:
09 Mar 05 (Deposition) - 22 Mar 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Psi, Secsg, Ubiquitin-Conjugating Enzyme, Caenorhabditis Elegans, Proteosome Pathway, Structural Genomics, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. A. Gavira, E. Digiamamarino, W. Tempel, Z. J. Liu, B. C. Wang, E. Meehan, J. D. Ng
The 1. 1A Crystallographic Structure Of Ubiquitin-Conjugating Enzyme (Ubc-2) From Caenorhabditis Elegans: Functional And Evolutionary Significance
To Be Published
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 19)
Info
All Hetero Components
1a: (R,R)-2,3-BUTANEDIOL (BU3a)
1b: (R,R)-2,3-BUTANEDIOL (BU3b)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: SODIUM ION (NAa)
4a: UNKNOWN ATOM OR ION (UNXa)
4b: UNKNOWN ATOM OR ION (UNXb)
4c: UNKNOWN ATOM OR ION (UNXc)
4d: UNKNOWN ATOM OR ION (UNXd)
4e: UNKNOWN ATOM OR ION (UNXe)
4f: UNKNOWN ATOM OR ION (UNXf)
4g: UNKNOWN ATOM OR ION (UNXg)
4h: UNKNOWN ATOM OR ION (UNXh)
4i: UNKNOWN ATOM OR ION (UNXi)
4j: UNKNOWN ATOM OR ION (UNXj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BU3
2
Ligand/Ion
(R,R)-2,3-BUTANEDIOL
2
CL
6
Ligand/Ion
CHLORIDE ION
3
NA
1
Ligand/Ion
SODIUM ION
4
UNX
10
Ligand/Ion
UNKNOWN ATOM OR ION
[
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]
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
THR A:58 , ASP A:59 , LYS A:63 , UNX A:502
BINDING SITE FOR RESIDUE CL A 601
02
AC2
SOFTWARE
SER A:-1 , ARG A:131 , LYS A:144 , HOH A:318
BINDING SITE FOR RESIDUE CL A 602
03
AC3
SOFTWARE
HIS A:0 , LEU A:3 , ARG A:131 , HOH A:315 , HOH A:356
BINDING SITE FOR RESIDUE CL A 603
04
AC4
SOFTWARE
ARG A:15
BINDING SITE FOR RESIDUE CL A 604
05
AC5
SOFTWARE
GLY A:-2 , HIS A:0 , LYS A:4 , MET A:147
BINDING SITE FOR RESIDUE CL A 605
06
AC6
SOFTWARE
BU3 A:201 , HOH A:317 , HOH A:334
BINDING SITE FOR RESIDUE CL A 606
07
AC7
SOFTWARE
SER A:-1 , ASP A:112 , PRO A:113 , TYR A:127 , BU3 A:201
BINDING SITE FOR RESIDUE NA A 701
08
AC8
SOFTWARE
SER A:-1 , ASP A:112 , PRO A:113 , PRO A:115 , ASP A:116 , HOH A:319 , HOH A:353 , CL A:606 , NA A:701
BINDING SITE FOR RESIDUE BU3 A 201
09
AC9
SOFTWARE
ARG A:15 , HOH A:383 , HOH A:404
BINDING SITE FOR RESIDUE BU3 A 202
10
BC1
SOFTWARE
ASP A:28 , ASP A:29 , LEU A:30 , PHE A:31 , ARG A:139
BINDING SITE FOR RESIDUE UNX A 501
11
BC2
SOFTWARE
CL A:601
BINDING SITE FOR RESIDUE UNX A 502
12
BC3
SOFTWARE
ASP A:130
BINDING SITE FOR RESIDUE UNX A 503
13
BC4
SOFTWARE
SER A:22 , THR A:36
BINDING SITE FOR RESIDUE UNX A 504
14
BC5
SOFTWARE
LEU A:86 , ASN A:114 , HOH A:364
BINDING SITE FOR RESIDUE UNX A 505
15
BC6
SOFTWARE
VAL A:26 , ASP A:29 , SER A:94 , ARG A:139 , UNX A:508 , UNX A:509
BINDING SITE FOR RESIDUE UNX A 506
16
BC7
SOFTWARE
GLN A:34 , ALA A:35 , THR A:36
BINDING SITE FOR RESIDUE UNX A 507
17
BC8
SOFTWARE
GLY A:27 , ASP A:28 , ALA A:96 , ARG A:139 , UNX A:506
BINDING SITE FOR RESIDUE UNX A 508
18
BC9
SOFTWARE
HIS A:32 , SER A:94 , UNX A:506 , UNX A:510
BINDING SITE FOR RESIDUE UNX A 509
19
CC1
SOFTWARE
GLN A:136 , UNX A:509
BINDING SITE FOR RESIDUE UNX A 510
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_UBC2_CAEEL_001 (H75Y, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_UBC2_CAEEL_001
*
H
75
Y
UBC2_CAEEL
---
---
A
H
75
Y
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_CONJUGAT_2 (A:4-136)
2: UBIQUITIN_CONJUGAT_1 (A:74-89)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_CONJUGAT_2
PS50127
Ubiquitin-conjugating enzymes family profile.
UBC2_CAEEL
4-136
1
A:4-136
2
UBIQUITIN_CONJUGAT_1
PS00183
Ubiquitin-conjugating enzymes active site.
UBC2_CAEEL
74-89
1
A:74-89
[
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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, 1)
Info
All SCOP Domains
1a: SCOP_d1z2ua1 (A:1-147)
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Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
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(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
UBC-like
(176)
Superfamily
:
UBC-like
(176)
Family
:
UBC-related
(135)
Protein domain
:
Ubiquitin conjugating enzyme, UBC
(84)
Caenorhabditis elegans, E2 2 [TaxId: 6239]
(1)
1a
d1z2ua1
A:1-147
[
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1z2uA00 (A:-2-147)
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Architectures
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Topologies
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)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin Conjugating Enzyme
(83)
Homologous Superfamily
:
Ubiquitin Conjugating Enzyme
(83)
Caenorhabditis elegans. Organism_taxid: 6239.
(4)
1a
1z2uA00
A:-2-147
[
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]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_UQ_con_1z2uA01 (A:5-142)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
UBC
(69)
Family
:
UQ_con
(55)
Caenorhabditis elegans
(4)
1a
UQ_con-1z2uA01
A:5-142
[
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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select chains 'A' and 'C'
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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
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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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Asym.Unit (62 KB)
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