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2K03
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Models
(20 )
Title
:
STRUCTURE OF SDF1 IN COMPLEX WITH THE CXCR4 N-TERMINUS CONTAINING A SULFOTYROSINE AT POSTITION 21
Authors
:
B. F. Volkman, C. T. Veldkamp, F. C. Peterson
Date
:
24 Jan 08 (Deposition) - 28 Oct 08 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A,B,C,D (20 x)
Keywords
:
Stromal Cell Derived Factor-1, Sdf1-Alpha, Cxcl12, Cxcr4, Chemokine, Sulfotyrosine, Locked Dimer, Alternative Splicing, Chemotaxis, Cytokine, Growth Factor, Secreted, G- Protein Coupled Receptor, Glycoprotein, Host-Virus Interaction, Membrane, Receptor, Sulfation, Transducer, Transmembrane
(Keyword Search:
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Reference
:
C. T. Veldkamp, C. Seibert, F. C. Peterson, N. B. De La Cruz, J. C. Haugner, H. Basnet, T. P. Sakmar, B. F. Volkman
Structural Basis Of Cxcr4 Sulfotyrosine Recognition By The Chemokine Sdf-1/Cxcl12
Sci. Signal. V. 1 Ra4 2008
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: O-SULFO-L-TYROSINE (TYSa)
1b: O-SULFO-L-TYROSINE (TYSb)
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Label:
No.
Name
Count
Type
Full Name
1
TYS
2
Mod. Amino Acid
O-SULFO-L-TYROSINE
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Sites
(0, 0)
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SAPs(SNPs)/Variants
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(3, 6)
Info
All Exons
Exon 1.3b (A:1-39 | C:201-239)
Exon 1.4a (A:39-68 | C:239-268)
Exon 1.6a (A:68-68 | C:268-268)
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1: Boundary 1.2a/1.3b
2: Boundary 1.3b/1.4a
3: Boundary 1.4a/1.6a
4: Boundary 1.6a/-
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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
1.2a
ENST00000374429
2a
ENSE00001463492
chr10:
44880540-44880393
148
SDF1_HUMAN
1-21
21
0
-
-
1.3b
ENST00000374429
3b
ENSE00000701629
chr10:
44876328-44876211
118
SDF1_HUMAN
21-60
40
2
A:1-39
C:201-239
39
39
1.4a
ENST00000374429
4a
ENSE00001463490
chr10:
44874171-44874085
87
SDF1_HUMAN
60-89
30
2
A:39-68
C:239-268
30
30
1.6a
ENST00000374429
6a
ENSE00001902365
chr10:
44868791-44865613
3179
SDF1_HUMAN
89-93
5
2
A:68-68
C:268-268
1
1
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SCOP Domains
(1, 2)
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1a: SCOP_d2k03a_ (A:)
1b: SCOP_d2k03c_ (C:)
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Protein Domains
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(
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Organisms
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(
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Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
IL8-like
(118)
Superfamily
:
Interleukin 8-like chemokines
(117)
Family
:
Interleukin 8-like chemokines
(113)
Protein domain
:
automated matches
(22)
Human (Homo sapiens) [TaxId: 9606]
(21)
1a
d2k03a_
A:
1b
d2k03c_
C:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2k03A00 (A:1-68)
1b: CATH_2k03C00 (C:201-268)
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(
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Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.40, no name defined]
(161)
Human (Homo sapiens)
(86)
1a
2k03A00
A:1-68
1b
2k03C00
C:201-268
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_CXCR4_N_2k03D01 (D:306-338)
1b: PFAM_CXCR4_N_2k03D02 (D:306-338)
2a: PFAM_IL8_2k03C01 (C:203-266)
2b: PFAM_IL8_2k03C02 (C:203-266)
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(
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Clan
:
no clan defined [family: CXCR4_N]
(8)
Family
:
CXCR4_N
(8)
Homo sapiens (Human)
(8)
1a
CXCR4_N-2k03D01
D:306-338
1b
CXCR4_N-2k03D02
D:306-338
Clan
:
no clan defined [family: IL8]
(55)
Family
:
IL8
(55)
Homo sapiens (Human)
(49)
2a
IL8-2k03C01
C:203-266
2b
IL8-2k03C02
C:203-266
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