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2BC4
Biol. Unit 1
Info
Asym.Unit (142 KB)
Biol.Unit 1 (69 KB)
Biol.Unit 2 (71 KB)
Biol.Unit 3 (136 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HLA-DM
Authors
:
M. J. Nicholson, B. Moradi, N. P. Seth, X. Xing, G. D. Cuny, R. L. Stein, K. W. Wucherpfennig
Date
:
18 Oct 05 (Deposition) - 23 May 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.27
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Mhc Class Ii, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Nicholson, B. Moradi, N. P. Seth, X. Xing, G. D. Cuny, R. L. Stein, K. W. Wucherpfennig
Small Molecules That Enhance The Catalytic Efficiency Of Hla-Dm.
J. Immunol. V. 176 4208 2006
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
3b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
3c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
3d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC9 (SOFTWARE)
9: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:13 , ASN A:15 , NDG A:213 , HOH A:509 , HOH A:542 , LEU B:12 , LYS B:20 , VAL D:50
BINDING SITE FOR RESIDUE NDG A 212
2
AC2
SOFTWARE
NDG A:212 , BMA A:214 , LYS B:20
BINDING SITE FOR RESIDUE NDG A 213
3
AC3
SOFTWARE
NDG A:213 , BMA A:215 , ASN D:52
BINDING SITE FOR RESIDUE BMA A 214
4
AC4
SOFTWARE
ASP A:200 , BMA A:214
BINDING SITE FOR RESIDUE BMA A 215
5
AC5
SOFTWARE
GLY B:49 , VAL B:50 , ASP C:12 , LEU C:13 , ASN C:15 , NDG C:213 , HOH C:510 , HOH C:543 , HOH C:611 , LEU D:12 , LYS D:20 , GLY D:192 , PRO D:195
BINDING SITE FOR RESIDUE NDG C 212
6
AC6
SOFTWARE
PHE B:48 , GLY B:49 , VAL B:50 , NDG C:212 , BMA C:214 , LYS D:20 , TYR D:168 , GLY D:192 , LEU D:193
BINDING SITE FOR RESIDUE NDG C 213
7
AC7
SOFTWARE
ASN B:52 , SER B:53 , NDG C:213 , BMA C:215
BINDING SITE FOR RESIDUE BMA C 214
8
AC9
SOFTWARE
HIS B:145
BINDING SITE FOR RESIDUE CL B 501
9
BC1
SOFTWARE
ARG A:98
BINDING SITE FOR RESIDUE CL D 502
[
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]
SAPs(SNPs)/Variants
(13, 13)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_050360 (T10A, chain B, )
02: VAR_016752 (S27F, chain B, )
03: VAR_050361 (D31V, chain B, )
04: VAR_050362 (S53N, chain B, )
05: VAR_016746 (Q136Q, chain A, )
06: VAR_016747 (H137H, chain A, )
07: VAR_016748 (V140I, chain A, )
08: VAR_016753 (A144E, chain B, )
09: VAR_016754 (A144V, chain B, )
10: VAR_016749 (G155A, chain A, )
11: VAR_016755 (I179T, chain B, )
12: VAR_016750 (R184C, chain A, )
13: VAR_016751 (R184H, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_050360
T
28
A
DMB_HUMAN
Polymorphism
17583782
B
T
10
A
02
UniProt
VAR_016752
S
45
F
DMB_HUMAN
Polymorphism
41560814
B
S
27
F
03
UniProt
VAR_050361
D
49
V
DMB_HUMAN
Polymorphism
17617333
B
D
31
V
04
UniProt
VAR_050362
S
71
N
DMB_HUMAN
Polymorphism
17617321
B
S
53
N
05
UniProt
VAR_016746
H
162
Q
DMA_HUMAN
Polymorphism
---
A
Q
136
Q
06
UniProt
VAR_016747
D
163
H
DMA_HUMAN
Polymorphism
---
A
H
137
H
07
UniProt
VAR_016748
V
166
I
DMA_HUMAN
Polymorphism
1063478
A
V
140
I
08
UniProt
VAR_016753
A
162
E
DMB_HUMAN
Polymorphism
---
B
A
144
E
09
UniProt
VAR_016754
A
162
V
DMB_HUMAN
Polymorphism
---
B
A
144
V
10
UniProt
VAR_016749
G
181
A
DMA_HUMAN
Polymorphism
6926628
A
G
155
A
11
UniProt
VAR_016755
I
197
T
DMB_HUMAN
Polymorphism
1042337
B
I
179
T
12
UniProt
VAR_016750
R
210
C
DMA_HUMAN
Polymorphism
17214044
A
R
184
C
13
UniProt
VAR_016751
R
210
H
DMA_HUMAN
Polymorphism
41555121
A
R
184
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:172-178)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
DMB_HUMAN
190-196
1
B:172-178
-
DMA_HUMAN
200-206
1
A:174-180
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2bc4a2 (A:97-200)
1b: SCOP_d2bc4b2 (B:94-193)
1c: SCOP_d2bc4c2 (C:97-206)
1d: SCOP_d2bc4d2 (D:94-199)
2a: SCOP_d2bc4a1 (A:13-96)
2b: SCOP_d2bc4b1 (B:3-93)
2c: SCOP_d2bc4c1 (C:12-96)
2d: SCOP_d2bc4d1 (D:3-93)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
1a
d2bc4a2
A:97-200
1b
d2bc4b2
B:94-193
1c
d2bc4c2
C:97-206
1d
d2bc4d2
D:94-199
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
automated matches
(29)
Human (Homo sapiens) [TaxId: 9606]
(24)
2a
d2bc4a1
A:13-96
2b
d2bc4b1
B:3-93
2c
d2bc4c1
C:12-96
2d
d2bc4d1
D:3-93
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2bc4B01 (B:3-92)
1b: CATH_2bc4D01 (D:3-92)
1c: CATH_2bc4C01 (C:12-91)
1d: CATH_2bc4A01 (A:13-91)
2a: CATH_2bc4D02 (D:93-199)
2b: CATH_2bc4B02 (B:93-193)
2c: CATH_2bc4A02 (A:92-200)
2d: CATH_2bc4C02 (C:92-206)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
(75)
Homologous Superfamily
:
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
(75)
Human (Homo sapiens)
(48)
1a
2bc4B01
B:3-92
1b
2bc4D01
D:3-92
1c
2bc4C01
C:12-91
1d
2bc4A01
A:13-91
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2bc4D02
D:93-199
2b
2bc4B02
B:93-193
2c
2bc4A02
A:92-200
2d
2bc4C02
C:92-206
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Asymmetric Unit 1
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