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2EF1
Asym. Unit
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Asym.Unit (90 KB)
Biol.Unit 1 (45 KB)
Biol.Unit 2 (44 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN CD38
Authors
:
M. Kukimoto-Niino, O. Nureki, K. Murayama, M. Shirouzu, T. Katada, M. Hara-Yokoyama, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
20 Feb 07 (Deposition) - 27 Feb 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydrolase, Cell Sueface Antigen, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kukimoto-Niino, O. Nureki, K. Murayama, M. Shirouzu, T. Katada, M. Hara-Yokoyama, S. Yokoyama
Crystal Structure Of The Extracellular Domain Of Human Cd38
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
2
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:127 , LEU A:157 , THR A:158 , SER A:220 , THR A:221 , HOH A:345 , HOH A:355
BINDING SITE FOR RESIDUE EPE A 301
2
AC2
SOFTWARE
ARG B:127 , LEU B:157 , SER B:220 , THR B:221 , HOH B:340 , HOH B:347
BINDING SITE FOR RESIDUE EPE B 302
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_001323 (R140W, chain A/B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_001323
R
140
W
CD38_HUMAN
Polymorphism
1800561
A/B
R
140
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
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;
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End label:
Sorry, no Info available
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Exons
(8, 16)
Info
All Exons
Exon 1.1b (A:45-78 | B:45-78)
Exon 1.2a (A:78-121 | B:78-121)
Exon 1.3b (A:122-167 | B:122-167)
Exon 1.4 (A:167-195 | B:167-195)
Exon 1.5 (A:196-220 | B:196-220)
Exon 1.6 (A:220-251 | B:220-251 (gaps))
Exon 1.7b (A:251-280 | B:251-280)
Exon 1.8b (A:280-291 | B:280-289)
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All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.2a
3: Boundary 1.2a/1.3b
4: Boundary 1.3b/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7b
8: Boundary 1.7b/1.8b
9: Boundary 1.8b/-
View:
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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
1.1b
ENST00000226279
1b
ENSE00001131145
chr4:
15779901-15780270
370
CD38_HUMAN
1-78
78
2
A:45-78
B:45-78
34
34
1.2a
ENST00000226279
2a
ENSE00000705354
chr4:
15818134-15818263
130
CD38_HUMAN
78-121
44
2
A:78-121
B:78-121
44
44
1.3b
ENST00000226279
3b
ENSE00000705352
chr4:
15826504-15826639
136
CD38_HUMAN
122-167
46
2
A:122-167
B:122-167
46
46
1.4
ENST00000226279
4
ENSE00000404201
chr4:
15835840-15835925
86
CD38_HUMAN
167-195
29
2
A:167-195
B:167-195
29
29
1.5
ENST00000226279
5
ENSE00000705349
chr4:
15839715-15839788
74
CD38_HUMAN
196-220
25
2
A:196-220
B:196-220
25
25
1.6
ENST00000226279
6
ENSE00000705347
chr4:
15841649-15841741
93
CD38_HUMAN
220-251
32
2
A:220-251
B:220-251 (gaps)
32
32
1.7b
ENST00000226279
7b
ENSE00000404204
chr4:
15842075-15842161
87
CD38_HUMAN
251-280
30
2
A:251-280
B:251-280
30
30
1.8b
ENST00000226279
8b
ENSE00001131136
chr4:
15850162-15851069
908
CD38_HUMAN
280-300
21
2
A:280-291
B:280-289
12
10
[
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SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2ef1a1 (A:45-291)
2a: SCOP_d2ef1b_ (B:)
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Classes
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)
(
)
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)
(
)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
N-(deoxy)ribosyltransferase-like
(76)
Family
:
ADP ribosyl cyclase-like
(60)
Protein domain
:
ADP ribosyl cyclase
(42)
Human (Homo sapiens) [TaxId: 9606]
(33)
1a
d2ef1a1
A:45-291
Family
:
automated matches
(3)
Protein domain
:
automated matches
(3)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d2ef1b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2ef1A01 (A:45-116,A:144-199)
1b: CATH_2ef1B01 (B:45-116,B:144-199)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
ADP Ribosyl Cyclase; Chain A, domain 1
(29)
Homologous Superfamily
:
ADP Ribosyl Cyclase; Chain A, domain 1
(29)
Human (Homo sapiens)
(20)
1a
2ef1A01
A:45-116,A:144-199
1b
2ef1B01
B:45-116,B:144-199
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (90 KB)
Header - Asym.Unit
Biol.Unit 1 (45 KB)
Header - Biol.Unit 1
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