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2AZ5
Asym. Unit
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Asym.Unit (98 KB)
Biol.Unit 1 (93 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TNF-ALPHA WITH A SMALL MOLECULE INHIBITOR
Authors
:
M. M. He
Date
:
09 Sep 05 (Deposition) - 29 Nov 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Tnf-Alpha Trimer Disruption By Binding Of A Small Molecule Inhibitor, Cytokine
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. M. He, A. S. Smith, J. D. Oslob, W. M. Flanagan, A. C. Braisted, A. Whitty, M. T. Cancilla, J. Wang, A. A. Lugovskoy, J. C. Yoburn, A. D. Fung, G. Farrington, J. K. Eldredge, E. S. Day, L. A. Cruz, T. G. Cachero, S. K. Miller, J. E. Friedman, I. C. Choong, B. C. Cunningham
Small-Molecule Inhibition Of Tnf-Alpha.
Science V. 310 1022 2005
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: 6,7-DIMETHYL-3-[(METHYL{2-[METHYL(... (307a)
1b: 6,7-DIMETHYL-3-[(METHYL{2-[METHYL(... (307b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
307
2
Ligand/Ion
6,7-DIMETHYL-3-[(METHYL{2-[METHYL({1-[3-(TRIFLUOROMETHYL)PHENYL]-1H-INDOL-3-YL}METHYL)AMINO]ETHYL}AMINO)METHYL]-4H-CHROMEN-4-ONE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:57 , SER A:60 , TYR A:119 , LEU A:120 , GLY A:121 , GLY A:122 , TYR A:151 , TYR B:59 , TYR B:119 , LEU B:120 , GLY B:121 , TYR B:151
BINDING SITE FOR RESIDUE 307 A 1
2
AC2
SOFTWARE
LEU C:57 , SER C:60 , TYR C:119 , LEU C:120 , GLY C:121 , GLY C:122 , TYR C:151 , TYR D:59 , SER D:60 , TYR D:119 , LEU D:120 , GLY D:121
BINDING SITE FOR RESIDUE 307 C 2
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SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011927 (A18T, chain A/B/C/D, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011927
A
94
T
TNFA_HUMAN
Polymorphism
1800620
A/B/C/D
A
18
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: TNF_2 (A:13-157,B:13-157,C:13-157,D:13-15...)
2: TNF_1 (A:48-64,B:48-64,C:48-64,D:48-64)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TNF_2
PS50049
TNF family profile.
TNFA_HUMAN
89-233
4
A:13-157
B:13-157
C:13-157
D:13-157
2
TNF_1
PS00251
TNF family signature.
TNFA_HUMAN
124-140
4
A:48-64
B:48-64
C:48-64
D:48-64
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Exons
(2, 8)
Info
All Exons
Exon 1.13 (A:10-18 | B:10-18 | C:10-18 | D:10...)
Exon 1.14b (A:18-157 (gaps) | B:18-157 (gaps) ...)
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All Exon Boundaries
1: Boundary 1.12/1.13
2: Boundary 1.13/1.14b
3: Boundary 1.14b/-
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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
1.9f
ENST00000383496
9f
ENSE00001901059
HSCHR6_MHC_QBL:31533585-31533945
361
TNFA_HUMAN
1-62
62
0
-
-
1.12
ENST00000383496
12
ENSE00001626927
HSCHR6_MHC_QBL:31534554-31534599
46
TNFA_HUMAN
63-78
16
0
-
-
1.13
ENST00000383496
13
ENSE00001681816
HSCHR6_MHC_QBL:31534787-31534834
48
TNFA_HUMAN
78-94
17
4
A:10-18
B:10-18
C:10-18
D:10-18
9
9
9
9
1.14b
ENST00000383496
14b
ENSE00001902809
HSCHR6_MHC_QBL:31535136-31536356
1221
TNFA_HUMAN
94-233
140
4
A:18-157 (gaps)
B:18-157 (gaps)
C:18-157 (gaps)
D:18-157 (gaps)
140
140
140
140
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2az5a_ (A:)
1b: SCOP_d2az5b_ (B:)
1c: SCOP_d2az5c_ (C:)
1d: SCOP_d2az5d_ (D:)
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Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
TNF-like
(100)
Superfamily
:
TNF-like
(100)
Family
:
TNF-like
(82)
Protein domain
:
Tumor necrosis factor (TNF)
(14)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d2az5a_
A:
1b
d2az5b_
B:
1c
d2az5c_
C:
1d
d2az5d_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2az5D00 (D:10-157)
1b: CATH_2az5B00 (B:10-157)
1c: CATH_2az5A00 (A:10-157)
1d: CATH_2az5C00 (C:10-157)
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Organisms
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)
(
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Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.40, no name defined]
(56)
Human (Homo sapiens)
(38)
1a
2az5D00
D:10-157
1b
2az5B00
B:10-157
1c
2az5A00
A:10-157
1d
2az5C00
C:10-157
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Pfam Domains
(0, 0)
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all PFAM domains
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Asym.Unit (98 KB)
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