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Asym. Unit
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Asym.Unit (134 KB)
Biol.Unit 1 (127 KB)
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(1)
Title
:
STRUCTURE OF A PEPTIDE:N-GLYCANASE-RAD23 COMPLEX
Authors
:
J. -H. Lee, J. M. Choi, C. Lee, K. J. Yi, Y. Cho
Date
:
11 May 05 (Deposition) - 14 Jun 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Protein-Protein Complex, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. H. Lee, J. M. Choi, C. Lee, K. J. Yi, Y. Cho
Structure Of A Peptide:N-Glycanase-Rad23 Complex: Insight Into The Deglycosylation For Denatured Glycoproteins.
Proc. Natl. Acad. Sci. Usa V. 102 9144 2005
(for further references see the
PDB file header
)
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
2a: SUCROSE (SUCa)
2b: SUCROSE (SUCb)
2c: SUCROSE (SUCc)
3a: ZINC ION (ZNa)
View:
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No.
Name
Count
Type
Full Name
1
MSE
5
Mod. Amino Acid
SELENOMETHIONINE
2
SUC
3
Ligand/Ion
SUCROSE
3
ZN
1
Ligand/Ion
ZINC ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:238 , TRP A:251
BINDING SITE FOR RESIDUE SUC A 1001
2
AC2
SOFTWARE
GLU A:238 , GLN A:239 , SER A:240 , GLN A:243 , ILE A:246 , TRP A:251
BINDING SITE FOR RESIDUE SUC A 1002
3
AC3
SOFTWARE
TYR A:177 , ASN A:178 , GLY A:192 , GLU A:193 , ASN A:196 , TYR A:211 , HOH A:1004
BINDING SITE FOR RESIDUE SUC A 1003
4
AC4
SOFTWARE
CYS A:129 , CYS A:132 , CYS A:165 , CYS A:168
BINDING SITE FOR RESIDUE ZN A 999
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(2, 2)
Info
All Exons
Exon 1.1 (B:253-309)
Exon 2.1 (A:8-327)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
3: Boundary -/2.1
4: Boundary 2.1/-
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YEL037C
1
YEL037C.1
V:82603-81407
1197
RAD23_YEAST
1-398
398
1
B:253-309
57
2.1
YPL096W
1
YPL096W.1
XVI:366924-368015
1092
PNG1_YEAST
1-363
363
1
A:8-327
320
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SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1x3wb1 (B:253-309)
2a: SCOP_d1x3wa1 (A:8-327)
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
XPC-binding domain
(10)
Superfamily
:
XPC-binding domain
(10)
Family
:
XPC-binding domain
(8)
Protein domain
:
Rad23 STI1 domain
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
1a
d1x3wb1
B:253-309
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Transglutaminase core
(22)
Protein domain
:
Peptide:N-glycanase 1, PNG1
(2)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
2a
d1x3wa1
A:8-327
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Rad4_1x3wA01 (A:213-308)
2a: PFAM_XPC_binding_1x3wB01 (B:258-309)
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Clans
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(
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_CA
(169)
Family
:
Rad4
(5)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(5)
1a
Rad4-1x3wA01
A:213-308
Clan
:
no clan defined [family: XPC-binding]
(8)
Family
:
XPC-binding
(8)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(5)
2a
XPC-binding-1x3wB01
B:258-309
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Asymmetric Unit 1
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Asym.Unit (134 KB)
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