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Asym. Unit
Info
Asym.Unit (132 KB)
Biol.Unit 1 (125 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CD1A IN COMPLEX WITH A SYNTHETIC MYCOBACTIN LIPOPEPTIDE
Authors
:
D. M. Zajonc, M. D. Crispin, T. A. Bowden, D. C. Young, T. Y. Cheng, J. Hu, C. E. Costello, M. J. Miller, D. B. Moody, I. A. Wilson
Date
:
11 Nov 04 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Beta Sheet Platform, Mhc-Fold, Protein-Lipopeptide Complex, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Zajonc, M. D. Crispin, T. A. Bowden, D. C. Young, T. Y. Cheng, J. Hu, C. E. Costello, P. M. Rudd, R. A. Dwek, M. J. Miller, M. B. Brenner, D. B. Moody, I. A. Wilson
Molecular Mechanism Of Lipopeptide Presentation By Cd1A.
Immunity V. 22 209 2005
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
1b: ALPHA-L-FUCOSE (FUCb)
2a: 6-(HYDROXY-HEXADECANOYL-AMINO)-2-{... (JH0a)
2b: 6-(HYDROXY-HEXADECANOYL-AMINO)-2-{... (JH0b)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
2
JH0
2
Ligand/Ion
6-(HYDROXY-HEXADECANOYL-AMINO)-2-{[(4S)-2-(2-HYDROXY-PHENYL)-4,5-DIHYDRO-OXAZOLE-4-CARBONYL]-AMINO}-HEXANOIC ACID 2-[(3S)-1-(TERT-BUTYL-DIPHENYL-SILANYLOXY)-2-OXO-AZEPAN-3-YLCARBAMOYL]-(1S)-1-METHYL-ETHYL ESTER
3
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:57 , ARG A:168 , NAG A:502 , FUC A:531
BINDING SITE FOR RESIDUE NAG A 501
2
AC2
SOFTWARE
ARG A:168 , NAG A:501
BINDING SITE FOR RESIDUE NAG A 502
3
AC3
SOFTWARE
LEU A:171 , ASP A:175 , NAG A:501
BINDING SITE FOR RESIDUE FUC A 531
4
AC4
SOFTWARE
ASN C:57 , PHE C:58 , ARG C:168 , LEU C:171 , FUC C:532
BINDING SITE FOR RESIDUE NAG C 501
5
AC5
SOFTWARE
ASP C:175 , NAG C:501
BINDING SITE FOR RESIDUE FUC C 532
6
AC6
SOFTWARE
TRP A:14 , ARG A:73 , ARG A:76 , SER A:77 , GLY A:80 , ILE A:81 , TYR A:84 , VAL A:147 , LEU A:148 , ASN A:151 , GLU A:154 , THR A:158 , PHE A:169
BINDING SITE FOR RESIDUE JH0 A 601
7
AC7
SOFTWARE
VAL C:12 , TRP C:14 , HIS C:38 , ARG C:73 , SER C:77 , ILE C:81 , LEU C:148 , GLU C:154 , THR C:158 , LEU C:162 , CYS C:166
BINDING SITE FOR RESIDUE JH0 C 602
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_010209 (I13I, chain A/C, )
2: VAR_010210 (W51W, chain A/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_010209
T
30
I
CD1A_HUMAN
Polymorphism
2269714
A/C
I
13
I
2
UniProt
VAR_010210
C
68
W
CD1A_HUMAN
Polymorphism
2269715
A/C
W
51
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84,D:78-84)
;
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.
B2MG_HUMAN
98-104
2
B:78-84
D:78-84
[
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Exons
(3, 6)
Info
All Exons
Exon 1.2 (A:7-92 | C:8-92)
Exon 1.3 (A:92-185 | C:92-185)
Exon 1.4 (A:185-277 | C:185-277)
View:
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
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
1.1
ENST00000289429
1
ENSE00001446470
chr1:
158223927-158224517
591
CD1A_HUMAN
1-20
20
0
-
-
1.2
ENST00000289429
2
ENSE00001075814
chr1:
158224874-158225140
267
CD1A_HUMAN
20-109
90
2
A:7-92
C:8-92
86
85
1.3
ENST00000289429
3
ENSE00001039139
chr1:
158225794-158226072
279
CD1A_HUMAN
109-202
94
2
A:92-185
C:92-185
94
94
1.4
ENST00000289429
4
ENSE00001601429
chr1:
158226576-158226854
279
CD1A_HUMAN
202-295
94
2
A:185-277
C:185-277
93
93
1.5
ENST00000289429
5
ENSE00001039144
chr1:
158227211-158227301
91
CD1A_HUMAN
295-325
31
0
-
-
1.6
ENST00000289429
6
ENSE00001446468
chr1:
158227471-158228059
589
CD1A_HUMAN
325-327
3
0
-
-
[
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SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1xz0b_ (B:)
1b: SCOP_d1xz0d_ (D:)
2a: SCOP_d1xz0a1 (A:184-277)
2b: SCOP_d1xz0c1 (C:184-277)
3a: SCOP_d1xz0a2 (A:7-183)
3b: SCOP_d1xz0c2 (C:8-183)
View:
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Classes
(
)
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Folds
(
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(
)
Superfamilies
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)
(
)
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)
(
)
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
:
beta2-microglobulin
(530)
Human (Homo sapiens) [TaxId: 9606]
(350)
1a
d1xz0b_
B:
1b
d1xz0d_
D:
Protein domain
:
CD1, alpha-3 domain
(24)
Human (Homo sapiens), CD1b [TaxId: 9606]
(6)
2a
d1xz0a1
A:184-277
2b
d1xz0c1
C:184-277
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
:
CD1, alpha-1 and alpha-2 domains
(39)
Human (Homo sapiens), CD1b [TaxId: 9606]
(6)
3a
d1xz0a2
A:7-183
3b
d1xz0c2
C:8-183
[
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]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1xz0A01 (A:7-182)
1b: CATH_1xz0C01 (C:8-182)
2a: CATH_1xz0B00 (B:1-98)
2b: CATH_1xz0A02 (A:183-277)
2c: CATH_1xz0C02 (C:183-277)
2d: CATH_1xz0D00 (D:1-98)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
(402)
Homologous Superfamily
:
Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1
(400)
Human (Homo sapiens)
(249)
1a
1xz0A01
A:7-182
1b
1xz0C01
C:8-182
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1xz0B00
B:1-98
2b
1xz0A02
A:183-277
2c
1xz0C02
C:183-277
2d
1xz0D00
D:1-98
[
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_C1_set_1xz0D01 (D:11-92)
1b: PFAM_C1_set_1xz0D02 (D:11-92)
1c: PFAM_C1_set_1xz0C01 (C:193-274)
1d: PFAM_C1_set_1xz0C02 (C:193-274)
2a: PFAM_MHC_I_1xz0C03 (C:8-181)
2b: PFAM_MHC_I_1xz0C04 (C:8-181)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-1xz0D01
D:11-92
1b
C1-set-1xz0D02
D:11-92
1c
C1-set-1xz0C01
C:193-274
1d
C1-set-1xz0C02
C:193-274
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
2a
MHC_I-1xz0C03
C:8-181
2b
MHC_I-1xz0C04
C:8-181
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