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2BC4
Asym. Unit
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
]
Hetero Components
(3, 12)
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
4
Ligand/Ion
BETA-D-MANNOSE
2
CL
4
Ligand/Ion
CHLORIDE ION
3
NDG
4
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
AC2
SOFTWARE
NDG A:212 , BMA A:214 , LYS B:20
BINDING SITE FOR RESIDUE NDG A 213
03
AC3
SOFTWARE
NDG A:213 , BMA A:215 , ASN D:52
BINDING SITE FOR RESIDUE BMA A 214
04
AC4
SOFTWARE
ASP A:200 , BMA A:214
BINDING SITE FOR RESIDUE BMA A 215
05
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
06
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
07
AC7
SOFTWARE
ASN B:52 , SER B:53 , NDG C:213 , BMA C:215
BINDING SITE FOR RESIDUE BMA C 214
08
AC8
SOFTWARE
ASP C:200 , BMA C:214 , LEU D:193
BINDING SITE FOR RESIDUE BMA C 215
09
AC9
SOFTWARE
HIS B:145
BINDING SITE FOR RESIDUE CL B 501
10
BC1
SOFTWARE
ARG A:98
BINDING SITE FOR RESIDUE CL D 502
11
BC2
SOFTWARE
HOH C:542
BINDING SITE FOR RESIDUE CL C 504
[
close Site info
]
SAPs(SNPs)/Variants
(13, 26)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_050360 (T10A, chain B/D, )
02: VAR_016752 (S27F, chain B/D, )
03: VAR_050361 (D31V, chain B/D, )
04: VAR_050362 (S53N, chain B/D, )
05: VAR_016746 (Q136Q, chain A/C, )
06: VAR_016747 (H137H, chain A/C, )
07: VAR_016748 (V140I, chain A/C, )
08: VAR_016753 (A144E, chain B/D, )
09: VAR_016754 (A144V, chain B/D, )
10: VAR_016749 (G155A, chain A/C, )
11: VAR_016755 (I179T, chain B/D, )
12: VAR_016750 (R184C, chain A/C, )
13: VAR_016751 (R184H, chain A/C, )
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/D
T
10
A
02
UniProt
VAR_016752
S
45
F
DMB_HUMAN
Polymorphism
41560814
B/D
S
27
F
03
UniProt
VAR_050361
D
49
V
DMB_HUMAN
Polymorphism
17617333
B/D
D
31
V
04
UniProt
VAR_050362
S
71
N
DMB_HUMAN
Polymorphism
17617321
B/D
S
53
N
05
UniProt
VAR_016746
H
162
Q
DMA_HUMAN
Polymorphism
---
A/C
Q
136
Q
06
UniProt
VAR_016747
D
163
H
DMA_HUMAN
Polymorphism
---
A/C
H
137
H
07
UniProt
VAR_016748
V
166
I
DMA_HUMAN
Polymorphism
1063478
A/C
V
140
I
08
UniProt
VAR_016753
A
162
E
DMB_HUMAN
Polymorphism
---
B/D
A
144
E
09
UniProt
VAR_016754
A
162
V
DMB_HUMAN
Polymorphism
---
B/D
A
144
V
10
UniProt
VAR_016749
G
181
A
DMA_HUMAN
Polymorphism
6926628
A/C
G
155
A
11
UniProt
VAR_016755
I
197
T
DMB_HUMAN
Polymorphism
1042337
B/D
I
179
T
12
UniProt
VAR_016750
R
210
C
DMA_HUMAN
Polymorphism
17214044
A/C
R
184
C
13
UniProt
VAR_016751
R
210
H
DMA_HUMAN
Polymorphism
41555121
A/C
R
184
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:172-178,D:172-178,A:174-180,C:17...)
;
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
2
B:172-178
D:172-178
DMA_HUMAN
200-206
2
A:174-180
C:174-180
[
close PROSITE info
]
Exons
(6, 12)
Info
All Exons
Exon 1.15a (A:13-99 | C:12-99)
Exon 1.15e (A:99-192 | C:99-192)
Exon 1.15j (A:192-200 | C:192-206)
Exon 2.20a (B:3-95 | D:3-95)
Exon 2.20e (B:95-190 | D:95-190)
Exon 2.20i (B:190-193 | D:190-199)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.12a/1.15a
2: Boundary 1.15a/1.15e
3: Boundary 1.15e/1.15j
4: Boundary 1.15j/1.16d
5: Boundary 2.19a/2.20a
6: Boundary 2.20a/2.20e
7: Boundary 2.20e/2.20i
8: Boundary 2.20i/2.20k
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
1.12a
ENST00000383230
12a
ENSE00002182258
HSCHR6_MHC_SSTO:33010800-33010627
174
DMA_HUMAN
1-30
30
0
-
-
1.15a
ENST00000383230
15a
ENSE00001761558
HSCHR6_MHC_SSTO:33008481-33008197
285
DMA_HUMAN
30-125
96
2
A:13-99
C:12-99
87
88
1.15e
ENST00000383230
15e
ENSE00001659539
HSCHR6_MHC_SSTO:33007567-33007289
279
DMA_HUMAN
125-218
94
2
A:99-192
C:99-192
94
94
1.15j
ENST00000383230
15j
ENSE00002174862
HSCHR6_MHC_SSTO:33007077-33006949
129
DMA_HUMAN
218-261
44
2
A:192-200
C:192-206
9
15
1.16d
ENST00000383230
16d
ENSE00001818600
HSCHR6_MHC_SSTO:33006546-33006288
259
DMA_HUMAN
261-261
1
0
-
-
2.19a
ENST00000383231
19a
ENSE00001871999
HSCHR6_MHC_QBL:32837576-32837259
318
DMB_HUMAN
1-19
19
0
-
-
2.20a
ENST00000383231
20a
ENSE00001753767
HSCHR6_MHC_QBL:32835472-32835191
282
DMB_HUMAN
19-113
95
2
B:3-95
D:3-95
93
93
2.20e
ENST00000383231
20e
ENSE00002181255
HSCHR6_MHC_QBL:32833963-32833679
285
DMB_HUMAN
113-208
96
2
B:95-190
D:95-190
96
96
2.20i
ENST00000383231
20i
ENSE00001591922
HSCHR6_MHC_QBL:32832159-32832043
117
DMB_HUMAN
208-247
40
2
B:190-193
D:190-199
4
10
2.20k
ENST00000383231
20k
ENSE00001724215
HSCHR6_MHC_QBL:32831884-32831849
36
DMB_HUMAN
247-259
13
0
-
-
2.20n
ENST00000383231
20n
ENSE00001757202
HSCHR6_MHC_QBL:32831494-32831136
359
DMB_HUMAN
259-263
5
0
-
-
[
close EXON info
]
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
View:
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Label:
Sorry, no Info available
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Chain D
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Asym.Unit (142 KB)
Header - Asym.Unit
Biol.Unit 1 (69 KB)
Header - Biol.Unit 1
Biol.Unit 2 (71 KB)
Header - Biol.Unit 2
Biol.Unit 3 (136 KB)
Header - Biol.Unit 3
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