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2VYR
Asym. Unit
Info
Asym.Unit (234 KB)
Biol.Unit 1 (228 KB)
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(1)
Title
:
STRUCTURE OF HUMAN MDM4 N-TERMINAL DOMAIN BOUND TO A SINGLE DOMAIN ANTIBODY
Authors
:
G. W. Yu, M. Vaysburd, M. D. Allen, G. Settanni, A. R. Fersht
Date
:
28 Jul 08 (Deposition) - 25 Nov 08 (Release) - 06 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Nucleus, Human Mdm4, Immune System, Zinc-Finger
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
G. W. Yu, M. Vaysburd, M. D. Allen, G. Settanni, A. R. Fersht
Structure Of Human Mdm4 N-Terminal Domain Bound To A Single-Domain Antibody.
J. Mol. Biol. V. 385 1578 2009
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN B:71 , ASN F:52 , ARG F:54 , TYR F:56 , HOH F:2101 , HOH F:2102 , HOH F:2103
BINDING SITE FOR RESIDUE SO4 F1125
2
AC2
SOFTWARE
GLN D:71 , ASN H:52 , ARG H:54 , TYR H:56 , HOH H:2078 , HOH H:2079 , HOH H:2080 , HOH H:2081
BINDING SITE FOR RESIDUE SO4 H1126
3
AC3
SOFTWARE
ARG A:87 , GLN A:88 , SER A:89
BINDING SITE FOR RESIDUE SO4 A1110
4
AC4
SOFTWARE
ARG B:87 , GLN B:88 , SER B:89
BINDING SITE FOR RESIDUE SO4 B1110
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(4, 16)
Info
All Exons
Exon 1.2a (A:25-26 | B:25-26 | C:25-26 | D:25...)
Exon 1.3 (A:27-51 | B:27-51 | C:27-51 | D:27...)
Exon 1.4 (A:52-96 | B:52-96 | C:52-96 | D:52...)
Exon 1.5a (A:96-110 | B:96-110 | C:96-110 | D...)
View:
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All Exon Boundaries
1: Boundary 1.1a/1.2a
2: Boundary 1.2a/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5a
5: Boundary 1.5a/1.8a
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
1.1a
ENST00000367182
1a
ENSE00001443738
chr1:
204485511-204485637
127
MDM4_HUMAN
-
0
0
-
-
1.2a
ENST00000367182
2a
ENSE00002156140
chr1:
204494612-204494724
113
MDM4_HUMAN
1-26
26
4
A:25-26
B:25-26
C:25-26
D:25-26
2
2
2
2
1.3
ENST00000367182
3
ENSE00001039934
chr1:
204495488-204495562
75
MDM4_HUMAN
27-51
25
4
A:27-51
B:27-51
C:27-51
D:27-51
25
25
25
25
1.4
ENST00000367182
4
ENSE00001039926
chr1:
204499812-204499945
134
MDM4_HUMAN
52-96
45
4
A:52-96
B:52-96
C:52-96
D:52-96
45
45
45
45
1.5a
ENST00000367182
5a
ENSE00001039924
chr1:
204501319-204501374
56
MDM4_HUMAN
96-115
20
4
A:96-110
B:96-110
C:96-110
D:96-110
15
15
15
15
1.8a
ENST00000367182
8a
ENSE00001039927
chr1:
204506558-204506625
68
MDM4_HUMAN
115-137
23
0
-
-
1.9d
ENST00000367182
9d
ENSE00001039922
chr1:
204507337-204507436
100
MDM4_HUMAN
138-171
34
0
-
-
1.10b
ENST00000367182
10b
ENSE00001075004
chr1:
204511912-204512072
161
MDM4_HUMAN
171-224
54
0
-
-
1.11b
ENST00000367182
11b
ENSE00001074998
chr1:
204513663-204513812
150
MDM4_HUMAN
225-274
50
0
-
-
1.12b
ENST00000367182
12b
ENSE00001075005
chr1:
204515925-204516005
81
MDM4_HUMAN
275-301
27
0
-
-
1.13e
ENST00000367182
13e
ENSE00001123001
chr1:
204518241-204527248
9008
MDM4_HUMAN
302-490
189
0
-
-
[
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SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2vyra_ (A:)
1b: SCOP_d2vyrb_ (B:)
1c: SCOP_d2vyrc_ (C:)
1d: SCOP_d2vyrd_ (D:)
2a: SCOP_d2vyre_ (E:)
2b: SCOP_d2vyrf_ (F:)
2c: SCOP_d2vyrg_ (G:)
2d: SCOP_d2vyrh_ (H:)
2e: SCOP_d2vyri_ (I:)
2f: SCOP_d2vyrj_ (J:)
2g: SCOP_d2vyrk_ (K:)
2h: SCOP_d2vyrl_ (L:)
View:
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)
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
SWIB/MDM2 domain
(62)
Superfamily
:
SWIB/MDM2 domain
(62)
Family
:
automated matches
(10)
Protein domain
:
automated matches
(10)
Human (Homo sapiens) [TaxId: 9606]
(10)
1a
d2vyra_
A:
1b
d2vyrb_
B:
1c
d2vyrc_
C:
1d
d2vyrd_
D:
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
automated matches
(311)
Human (Homo sapiens) [TaxId: 9606]
(85)
2a
d2vyre_
E:
2b
d2vyrf_
F:
2c
d2vyrg_
G:
2d
d2vyrh_
H:
2e
d2vyri_
I:
2f
d2vyrj_
J:
2g
d2vyrk_
K:
2h
d2vyrl_
L:
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2vyrA00 (A:25-110)
1b: CATH_2vyrB00 (B:25-110)
1c: CATH_2vyrC00 (C:25-110)
1d: CATH_2vyrD00 (D:25-110)
2a: CATH_2vyrG00 (G:1-123)
2b: CATH_2vyrE00 (E:1-124)
2c: CATH_2vyrF00 (F:1-124)
2d: CATH_2vyrI00 (I:1-124)
2e: CATH_2vyrJ00 (J:1-124)
2f: CATH_2vyrK00 (K:1-124)
2g: CATH_2vyrL00 (L:1-124)
2h: CATH_2vyrH00 (H:1-125)
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)
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Architectures
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)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
MDM2
(34)
Homologous Superfamily
:
MDM2
(34)
Human (Homo sapiens)
(22)
1a
2vyrA00
A:25-110
1b
2vyrB00
B:25-110
1c
2vyrC00
C:25-110
1d
2vyrD00
D:25-110
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2vyrG00
G:1-123
2b
2vyrE00
E:1-124
2c
2vyrF00
F:1-124
2d
2vyrI00
I:1-124
2e
2vyrJ00
J:1-124
2f
2vyrK00
K:1-124
2g
2vyrL00
L:1-124
2h
2vyrH00
H:1-125
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_SWIB_2vyrD01 (D:26-101)
1b: PFAM_SWIB_2vyrD02 (D:26-101)
1c: PFAM_SWIB_2vyrD03 (D:26-101)
1d: PFAM_SWIB_2vyrD04 (D:26-101)
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Clan
:
no clan defined [family: SWIB]
(22)
Family
:
SWIB
(22)
Homo sapiens (Human)
(15)
1a
SWIB-2vyrD01
D:26-101
1b
SWIB-2vyrD02
D:26-101
1c
SWIB-2vyrD03
D:26-101
1d
SWIB-2vyrD04
D:26-101
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Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
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