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3G76
Asym. Unit
Info
Asym.Unit (322 KB)
Biol.Unit 1 (40 KB)
Biol.Unit 2 (42 KB)
Biol.Unit 3 (39 KB)
Biol.Unit 4 (43 KB)
Biol.Unit 5 (47 KB)
Biol.Unit 6 (42 KB)
Biol.Unit 7 (40 KB)
Biol.Unit 8 (43 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF XIAP-BIR3 IN COMPLEX WITH A BIVALENT COMPOUND
Authors
:
F. Cossu, M. Milani, E. Mastrangelo, M. Bolognesi
Date
:
09 Feb 09 (Deposition) - 12 May 09 (Release) - 27 Oct 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Keywords
:
Apoptosis, Iap, Smacdiablo, Peptidomimetics, Pro-Apoptotic Drugs, Cytoplasm, Ligase, Metal-Binding, Phosphoprotein, Polymorphism, Protease Inhibitor, Thiol Protease Inhibitor, Ubl Conjugation, Ubl Conjugation Pathway, Zinc, Zinc-Finger
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Cossu, M. Milani, E. Mastrangelo, P. Vachette, F. Servida, D. Lecis, G. Canevari, D. Delia, C. Drago, V. Rizzo, L. Manzoni, P. Seneci, C. Scolastico, M. Bolognesi
Structural Basis For Bivalent Smac-Mimetics Recognition In The Iap Protein Family
J. Mol. Biol. V. 392 630 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: 1,1'-{HEXA-2,4-DIYNE-1,6-DIYLBIS[O... (CZ3a)
1b: 1,1'-{HEXA-2,4-DIYNE-1,6-DIYLBIS[O... (CZ3b)
1c: 1,1'-{HEXA-2,4-DIYNE-1,6-DIYLBIS[O... (CZ3c)
1d: 1,1'-{HEXA-2,4-DIYNE-1,6-DIYLBIS[O... (CZ3d)
1e: 1,1'-{HEXA-2,4-DIYNE-1,6-DIYLBIS[O... (CZ3e)
1f: 1,1'-{HEXA-2,4-DIYNE-1,6-DIYLBIS[O... (CZ3f)
1g: 1,1'-{HEXA-2,4-DIYNE-1,6-DIYLBIS[O... (CZ3g)
1h: 1,1'-{HEXA-2,4-DIYNE-1,6-DIYLBIS[O... (CZ3h)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CZ3
8
Ligand/Ion
1,1'-{HEXA-2,4-DIYNE-1,6-DIYLBIS[OXY{(2S,3R)-2-[(N-METHYL-L-ALANYL)AMINO]-1-OXOBUTANE-3,1-DIYL}(2S)PYRROLIDINE-1,2-DIYLMETHANEDIYL]}BIS[5-(PHENYLSULFANYL)-1H-TETRAZOLE]
2
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:300 , CYS A:303 , HIS A:320 , CYS A:327
BINDING SITE FOR RESIDUE ZN A 502
02
AC2
SOFTWARE
HOH A:90 , LEU A:292 , VAL A:298 , GLY A:306 , LEU A:307 , THR A:308 , ASP A:309 , TRP A:310 , GLU A:314 , GLN A:319 , TRP A:323 , TYR A:324 , PHE D:270 , HOH E:468
BINDING SITE FOR RESIDUE CZ3 A 600
03
AC3
SOFTWARE
CYS B:300 , CYS B:303 , HIS B:320 , CYS B:327
BINDING SITE FOR RESIDUE ZN B 502
04
AC4
SOFTWARE
LEU B:292 , LYS B:297 , VAL B:298 , GLY B:306 , LEU B:307 , THR B:308 , GLU B:314 , GLN B:319 , TRP B:323 , TYR B:324 , CZ3 D:600
BINDING SITE FOR RESIDUE CZ3 B 600
05
AC5
SOFTWARE
CYS C:300 , CYS C:303 , HIS C:320 , CYS C:327
BINDING SITE FOR RESIDUE ZN C 502
06
AC6
SOFTWARE
PHE B:270 , HOH C:107 , LEU C:292 , LYS C:297 , VAL C:298 , GLY C:306 , LEU C:307 , THR C:308 , ASP C:309 , TRP C:310 , GLU C:314 , GLN C:319 , TRP C:323 , TYR C:324
BINDING SITE FOR RESIDUE CZ3 C 600
07
AC7
SOFTWARE
CYS D:300 , CYS D:303 , HIS D:320 , CYS D:327
BINDING SITE FOR RESIDUE ZN D 502
08
AC8
SOFTWARE
CZ3 B:600 , HOH D:49 , HOH D:69 , LEU D:292 , GLY D:306 , LEU D:307 , THR D:308 , ASP D:309 , GLU D:314 , GLN D:319 , TRP D:323 , TYR D:324
BINDING SITE FOR RESIDUE CZ3 D 600
09
AC9
SOFTWARE
CYS E:300 , CYS E:303 , HIS E:320 , CYS E:327
BINDING SITE FOR RESIDUE ZN E 502
10
BC1
SOFTWARE
HOH E:1 , HOH E:22 , VAL E:298 , LYS E:299 , GLY E:306 , LEU E:307 , THR E:308 , ASP E:309 , LYS E:311 , GLU E:314 , GLN E:319 , TRP E:323 , TYR E:324 , HOH E:413 , PHE H:270
BINDING SITE FOR RESIDUE CZ3 E 600
11
BC2
SOFTWARE
CYS F:300 , CYS F:303 , HIS F:320 , CYS F:327
BINDING SITE FOR RESIDUE ZN F 502
12
BC3
SOFTWARE
LYS F:297 , GLY F:306 , LEU F:307 , THR F:308 , ASP F:309 , TRP F:310 , GLU F:314 , GLN F:319 , TRP F:323 , TYR F:324 , ARG F:354 , ASP H:309 , CZ3 H:600
BINDING SITE FOR RESIDUE CZ3 F 600
13
BC4
SOFTWARE
CYS G:300 , CYS G:303 , HIS G:320 , CYS G:327
BINDING SITE FOR RESIDUE ZN G 502
14
BC5
SOFTWARE
HOH E:446 , PHE F:270 , HOH G:24 , LYS G:297 , VAL G:298 , GLY G:306 , LEU G:307 , THR G:308 , ASP G:309 , LYS G:311 , GLU G:314 , GLN G:319 , TRP G:323 , TYR G:324
BINDING SITE FOR RESIDUE CZ3 G 600
15
BC6
SOFTWARE
CYS H:300 , CYS H:303 , HIS H:320 , CYS H:327
BINDING SITE FOR RESIDUE ZN H 502
16
BC7
SOFTWARE
HOH F:140 , ASP F:309 , CZ3 F:600 , HOH H:14 , LYS H:297 , GLY H:306 , LEU H:307 , THR H:308 , ASP H:309 , LYS H:311 , GLU H:314 , GLN H:319 , TRP H:323 , TYR H:324
BINDING SITE FOR RESIDUE CZ3 H 600
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 16)
Info
All PROSITE Patterns/Profiles
1: BIR_REPEAT_1 (-|-|A:265-330,B:265-330,C:265-330,...)
2: BIR_REPEAT_2 (-|-|A:268-331,B:268-331,C:268-331,...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BIR_REPEAT_1
PS01282
BIR repeat.
XIAP_HUMAN
26-93
163-230
265-330
8
-
-
A:265-330
B:265-330
C:265-330
D:265-330
E:265-330
F:265-330
G:265-330
H:265-330
2
BIR_REPEAT_2
PS50143
BIR repeat profile.
XIAP_HUMAN
29-94
166-231
268-331
8
-
-
A:268-331
B:268-331
C:268-331
D:268-331
E:268-331
F:268-331
G:268-331
H:268-331
[
close PROSITE info
]
Exons
(4, 28)
Info
All Exons
Exon 1.3c (A:252-293 | B:253-293 | C:253-293 ...)
Exon 1.4b (A:293-326 | B:293-326 | C:293-326 ...)
Exon 1.5b (A:326-348 | B:326-352 | C:326-348 ...)
Exon 1.6 (- | B:353-357 | - | D:353-357 | - ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2a/1.3c
2: Boundary 1.3c/1.4b
3: Boundary 1.4b/1.5b
4: Boundary 1.5b/1.6
5: Boundary 1.6/1.7b
View:
Label:
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
1.2a
ENST00000371199
2a
ENSE00001810722
X:122993877-122994143
267
XIAP_HUMAN
-
0
0
-
-
1.3c
ENST00000371199
3c
ENSE00002176074
X:123019481-123020389
909
XIAP_HUMAN
1-293
293
8
A:252-293
B:253-293
C:253-293
D:253-293
E:253-293
F:255-293
G:253-293
H:253-293
42
41
41
41
41
39
41
41
1.4b
ENST00000371199
4b
ENSE00001649641
X:123022469-123022568
100
XIAP_HUMAN
293-326
34
8
A:293-326
B:293-326
C:293-326
D:293-326
E:293-326
F:293-326
G:293-326
H:293-326
34
34
34
34
34
34
34
34
1.5b
ENST00000371199
5b
ENSE00001630752
X:123025088-123025166
79
XIAP_HUMAN
326-352
27
8
A:326-348
B:326-352
C:326-348
D:326-352
E:326-347
F:326-352
G:326-347
H:326-352
23
27
23
27
22
27
22
27
1.6
ENST00000371199
6
ENSE00001714518
X:123026581-123026623
43
XIAP_HUMAN
353-367
15
4
-
B:353-357
-
D:353-357
-
F:353-358
-
H:353-357
-
5
-
5
-
6
-
5
1.7b
ENST00000371199
7b
ENSE00001653318
X:123034343-123034543
201
XIAP_HUMAN
367-434
68
0
-
-
1.8e
ENST00000371199
8e
ENSE00001454620
X:123040838-123047829
6992
XIAP_HUMAN
434-497
64
0
-
-
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3g76a_ (A:)
1b: SCOP_d3g76b_ (B:)
1c: SCOP_d3g76c_ (C:)
1d: SCOP_d3g76d_ (D:)
1e: SCOP_d3g76e_ (E:)
1f: SCOP_d3g76f_ (F:)
1g: SCOP_d3g76g_ (G:)
1h: SCOP_d3g76h_ (H:)
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Classes
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)
(
)
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(
)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Inhibitor of apoptosis (IAP) repeat
(71)
Superfamily
:
Inhibitor of apoptosis (IAP) repeat
(71)
Family
:
Inhibitor of apoptosis (IAP) repeat
(70)
Protein domain
:
automated matches
(24)
Human (Homo sapiens) [TaxId: 9606]
(24)
1a
d3g76a_
A:
1b
d3g76b_
B:
1c
d3g76c_
C:
1d
d3g76d_
D:
1e
d3g76e_
E:
1f
d3g76f_
F:
1g
d3g76g_
G:
1h
d3g76h_
H:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_3g76F00 (F:255-358)
1b: CATH_3g76B00 (B:253-357)
1c: CATH_3g76D00 (D:253-357)
1d: CATH_3g76H00 (H:253-357)
1e: CATH_3g76A00 (A:252-348)
1f: CATH_3g76C00 (C:253-348)
1g: CATH_3g76E00 (E:253-347)
1h: CATH_3g76G00 (G:253-347)
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
(42)
Homologous Superfamily
:
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
(42)
Human (Homo sapiens)
(35)
1a
3g76F00
F:255-358
1b
3g76B00
B:253-357
1c
3g76D00
D:253-357
1d
3g76H00
H:253-357
1e
3g76A00
A:252-348
1f
3g76C00
C:253-348
1g
3g76E00
E:253-347
1h
3g76G00
G:253-347
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain H
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Asym.Unit (322 KB)
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Biol.Unit 2 (42 KB)
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Biol.Unit 3 (39 KB)
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Biol.Unit 4 (43 KB)
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Biol.Unit 5 (47 KB)
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