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3CM2
Asym. Unit
Info
Asym.Unit (194 KB)
Biol.Unit 1 (40 KB)
Biol.Unit 10 (22 KB)
Biol.Unit 11 (22 KB)
Biol.Unit 12 (22 KB)
Biol.Unit 13 (22 KB)
Biol.Unit 14 (22 KB)
Biol.Unit 15 (22 KB)
Biol.Unit 2 (40 KB)
Biol.Unit 3 (40 KB)
Biol.Unit 4 (40 KB)
Biol.Unit 5 (40 KB)
Biol.Unit 6 (22 KB)
Biol.Unit 7 (22 KB)
Biol.Unit 8 (22 KB)
Biol.Unit 9 (22 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF XIAP BIR3 DOMAIN IN COMPLEX WITH A SMAC-MIMETIC COMPOUND, SMAC010
Authors
:
F. Cossu, E. Mastrangelo, M. Milani
Date
:
20 Mar 08 (Deposition) - 28 Oct 08 (Release) - 09 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: D,F (1x)
Biol. Unit 2: A,J (1x)
Biol. Unit 3: B,H (1x)
Biol. Unit 4: C,I (1x)
Biol. Unit 5: E,G (1x)
Biol. Unit 6: A (1x)
Biol. Unit 7: B (1x)
Biol. Unit 8: C (1x)
Biol. Unit 9: D (1x)
Biol. Unit 10: E (1x)
Biol. Unit 11: F (1x)
Biol. Unit 12: G (1x)
Biol. Unit 13: H (1x)
Biol. Unit 14: I (1x)
Biol. Unit 15: J (1x)
Keywords
:
Zinc-Finger, Apoptosis, Cytoplasm, Ligase, Metal-Binding, Phosphoprotein, Polymorphism, Protease Inhibitor, Thiol Protease Inhibitor, Ubl Conjugation, Ubl Conjugation Pathway
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Mastrangelo, F. Cossu, M. Milani, G. Sorrentino, D. Lecis, D. Delia, L. Manzoni, C. Drago, P. Seneci, C. Scolastico, V. Rizzo, M. Bolognesi
Targeting The X-Linked Inhibitor Of Apoptosis Protein Through 4-Substituted Azabicyclo[5. 3. 0]Alkane Smac Mimetics. Structure, Activity, And Recognition Principles.
J. Mol. Biol. V. 384 673 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 20)
Info
All Hetero Components
1a: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23a)
1b: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23b)
1c: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23c)
1d: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23d)
1e: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23e)
1f: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23f)
1g: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23g)
1h: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23h)
1i: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23i)
1j: (3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUT... (X23j)
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)
2i: ZINC ION (ZNi)
2j: ZINC ION (ZNj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
X23
10
Ligand/Ion
(3S,6S,7R,9AS)-6-{[(2S)-2-AMINOBUTANOYL]AMINO}-7-(AMINOMETHYL)-N-(DIPHENYLMETHYL)-5-OXOOCTAHYDRO-1H-PYRROLO[1,2-A]AZEPINE-3-CARBOXAMIDE
2
ZN
10
Ligand/Ion
ZINC ION
[
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]
Sites
(20, 20)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS D:300 , CYS D:303 , HIS D:320 , CYS D:327
BINDING SITE FOR RESIDUE ZN D 502
02
AC2
SOFTWARE
CYS A:300 , CYS A:303 , HIS A:320 , CYS A:327
BINDING SITE FOR RESIDUE ZN A 502
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
CYS C:300 , CYS C:303 , HIS C:320 , CYS C:327
BINDING SITE FOR RESIDUE ZN C 502
05
AC5
SOFTWARE
CYS E:300 , CYS E:303 , HIS E:320 , CYS E:327
BINDING SITE FOR RESIDUE ZN E 502
06
AC6
SOFTWARE
CYS F:300 , CYS F:303 , HIS F:320 , CYS F:327
BINDING SITE FOR RESIDUE ZN F 502
07
AC7
SOFTWARE
CYS G:300 , CYS G:303 , HIS G:320 , CYS G:327
BINDING SITE FOR RESIDUE ZN G 502
08
AC8
SOFTWARE
CYS H:300 , CYS H:303 , HIS H:320 , CYS H:327
BINDING SITE FOR RESIDUE ZN H 502
09
AC9
SOFTWARE
CYS I:300 , CYS I:303 , HIS I:320 , CYS I:327
BINDING SITE FOR RESIDUE ZN I 502
10
BC1
SOFTWARE
CYS J:300 , CYS J:303 , HIS J:320 , CYS J:327
BINDING SITE FOR RESIDUE ZN J 502
11
BC2
SOFTWARE
LEU D:292 , LYS D:297 , GLY D:306 , LEU D:307 , THR D:308 , ASP D:309 , TRP D:310 , GLU D:314 , GLN D:319 , TRP D:323 , GLU H:349 , LEU H:352
BINDING SITE FOR RESIDUE X23 D 600
12
BC3
SOFTWARE
LEU A:292 , LYS A:297 , LYS A:299 , GLY A:306 , LEU A:307 , THR A:308 , ASP A:309 , GLU A:314 , GLN A:319 , TRP A:323 , GLU B:349 , LEU B:352
BINDING SITE FOR RESIDUE X23 A 600
13
BC4
SOFTWARE
LEU B:292 , LYS B:297 , GLY B:306 , LEU B:307 , THR B:308 , ASP B:309 , TRP B:310 , GLU B:314 , GLN B:319 , TRP B:323 , GLU F:349 , LEU F:352
BINDING SITE FOR RESIDUE X23 B 600
14
BC5
SOFTWARE
LEU C:292 , LYS C:297 , GLY C:306 , LEU C:307 , THR C:308 , ASP C:309 , TRP C:310 , GLU C:314 , TRP C:323 , GLU G:349 , LEU G:352
BINDING SITE FOR RESIDUE X23 C 600
15
BC6
SOFTWARE
LEU E:292 , LYS E:297 , GLY E:306 , LEU E:307 , THR E:308 , ASP E:309 , TRP E:310 , GLU E:314 , GLN E:319 , TRP E:323 , GLU I:349 , LEU I:352
BINDING SITE FOR RESIDUE X23 E 600
16
BC7
SOFTWARE
HIS C:346 , GLU C:349 , LEU C:352 , LEU F:292 , 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
BINDING SITE FOR RESIDUE X23 F 600
17
BC8
SOFTWARE
HIS A:346 , GLU A:349 , LEU A:352 , LEU G:292 , LYS G:297 , GLY G:306 , LEU G:307 , THR G:308 , ASP G:309 , TRP G:310 , GLU G:314 , GLN G:319 , TRP G:323
BINDING SITE FOR RESIDUE X23 G 600
18
BC9
SOFTWARE
LEU H:292 , LYS H:297 , GLY H:306 , LEU H:307 , THR H:308 , ASP H:309 , TRP H:310 , GLU H:314 , GLN H:319 , TRP H:323 , GLU J:349 , LEU J:352
BINDING SITE FOR RESIDUE X23 H 600
19
CC1
SOFTWARE
GLU D:349 , LEU D:352 , LEU I:292 , LYS I:297 , LYS I:299 , GLY I:306 , LEU I:307 , THR I:308 , ASP I:309 , TRP I:310 , GLU I:314 , GLN I:319 , TRP I:323
BINDING SITE FOR RESIDUE X23 I 600
20
CC2
SOFTWARE
HIS E:346 , GLU E:349 , LEU E:352 , LYS J:297 , GLY J:306 , LEU J:307 , THR J:308 , ASP J:309 , TRP J:310 , GLU J:314 , GLN J:319 , TRP J:323
BINDING SITE FOR RESIDUE X23 J 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
[
close SNP/Variant info
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PROSITE Patterns/Profiles
(2, 20)
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
10
-
-
A:265-330
B:265-330
C:265-330
D:265-330
E:265-330
F:265-330
G:265-330
H:265-330
I:265-330
J:265-330
2
BIR_REPEAT_2
PS50143
BIR repeat profile.
XIAP_HUMAN
29-94
166-231
268-331
10
-
-
A:268-331
B:268-331
C:268-331
D:268-331
E:268-331
F:268-331
G:268-331
H:268-331
I:268-331
J:268-331
[
close PROSITE info
]
Exons
(4, 40)
Info
All Exons
Exon 1.3c (A:253-293 | B:253-293 | C:253-293 ...)
Exon 1.4b (A:293-326 | B:293-326 | C:293-326 ...)
Exon 1.5b (A:326-352 | B:326-352 | C:326-352 ...)
Exon 1.6 (A:353-355 | B:353-355 | C:353-354 ...)
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
10
A:253-293
B:253-293
C:253-293
D:254-293
E:254-293
F:253-293
G:254-293
H:254-293
I:254-293
J:254-293
41
41
41
40
40
41
40
40
40
40
1.4b
ENST00000371199
4b
ENSE00001649641
X:123022469-123022568
100
XIAP_HUMAN
293-326
34
10
A:293-326
B:293-326
C:293-326
D:293-326
E:293-326
F:293-326
G:293-326
H:293-326
I:293-326
J:293-326
34
34
34
34
34
34
34
34
34
34
1.5b
ENST00000371199
5b
ENSE00001630752
X:123025088-123025166
79
XIAP_HUMAN
326-352
27
10
A:326-352
B:326-352
C:326-352
D:326-352
E:326-352
F:326-352
G:326-352
H:326-352
I:326-352
J:326-352
27
27
27
27
27
27
27
27
27
27
1.6
ENST00000371199
6
ENSE00001714518
X:123026581-123026623
43
XIAP_HUMAN
353-367
15
10
A:353-355
B:353-355
C:353-354
D:353-355
E:353-355
F:353-355
G:353-355
H:353-355
I:353-355
J:353-356
3
3
2
3
3
3
3
3
3
4
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, 10)
Info
All SCOP Domains
1a: SCOP_d3cm2a_ (A:)
1b: SCOP_d3cm2h_ (H:)
1c: SCOP_d3cm2i_ (I:)
1d: SCOP_d3cm2j_ (J:)
1e: SCOP_d3cm2b_ (B:)
1f: SCOP_d3cm2c_ (C:)
1g: SCOP_d3cm2d_ (D:)
1h: SCOP_d3cm2e_ (E:)
1i: SCOP_d3cm2f_ (F:)
1j: SCOP_d3cm2g_ (G:)
View:
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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
:
BIR domains of XIAP
(15)
Human (Homo sapiens) [TaxId: 9606]
(15)
1a
d3cm2a_
A:
1b
d3cm2h_
H:
1c
d3cm2i_
I:
1d
d3cm2j_
J:
1e
d3cm2b_
B:
1f
d3cm2c_
C:
1g
d3cm2d_
D:
1h
d3cm2e_
E:
1i
d3cm2f_
F:
1j
d3cm2g_
G:
[
close SCOP info
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CATH Domains
(1, 10)
Info
all CATH domains
1a: CATH_3cm2C00 (C:253-354)
1b: CATH_3cm2D00 (D:254-355)
1c: CATH_3cm2E00 (E:254-355)
1d: CATH_3cm2G00 (G:254-355)
1e: CATH_3cm2H00 (H:254-355)
1f: CATH_3cm2I00 (I:254-355)
1g: CATH_3cm2A00 (A:253-355)
1h: CATH_3cm2B00 (B:253-355)
1i: CATH_3cm2F00 (F:253-355)
1j: CATH_3cm2J00 (J:254-356)
View:
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(
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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
3cm2C00
C:253-354
1b
3cm2D00
D:254-355
1c
3cm2E00
E:254-355
1d
3cm2G00
G:254-355
1e
3cm2H00
H:254-355
1f
3cm2I00
I:254-355
1g
3cm2A00
A:253-355
1h
3cm2B00
B:253-355
1i
3cm2F00
F:253-355
1j
3cm2J00
J:254-356
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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