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1Z5L
Asym. Unit
Info
Asym.Unit (137 KB)
Biol.Unit 1 (66 KB)
Biol.Unit 2 (66 KB)
Biol.Unit 3 (127 KB)
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(1)
Title
:
STRUCTURE OF A HIGHLY POTENT SHORT-CHAIN GALACTOSYL CERAMIDE AGONIST BOUND TO CD1D
Authors
:
D. M. Zajonc, C. Cantu, J. Mattner, D. Zhou, P. B. Savage, A. Bendelac, I. L. Teyton
Date
:
18 Mar 05 (Deposition) - 19 Jul 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
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
:
Ig Fold, Mhc Fold, Immune System
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
D. M. Zajonc, C. Cantu, J. Mattner, D. Zhou, P. B. Savage, A. Bendelac, I. A. Wilson, L. Teyton
Structure And Function Of A Potent Agonist For The Semi-Invariant Natural Killer T Cell Receptor.
Nat. Immunol. V. 6 810 2005
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Hetero Components
(3, 11)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2a: (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-... (PBSa)
2b: (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-... (PBSb)
3a: HEXADECANE (R16a)
3b: HEXADECANE (R16b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
PBS
2
Ligand/Ion
(2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL
3
R16
2
Ligand/Ion
HEXADECANE
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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
ASN A:20 , SER A:22
BINDING SITE FOR RESIDUE NAG A 500
02
AC2
SOFTWARE
TRP A:23 , SER A:24 , ASN A:42
BINDING SITE FOR RESIDUE NAG A 501
03
AC3
SOFTWARE
GLN A:161 , ASN A:165 , PRO A:197 , NAG A:512 , ASP B:96
BINDING SITE FOR RESIDUE NAG A 511
04
AC4
SOFTWARE
TRP A:129 , GLY A:130 , NAG A:511
BINDING SITE FOR RESIDUE NAG A 512
05
AC5
SOFTWARE
TRP C:23 , SER C:24 , ASN C:42
BINDING SITE FOR RESIDUE NAG C 501
06
AC6
SOFTWARE
GLY C:130 , THR C:131 , GLN C:161 , ASN C:165 , PRO C:197 , NAG C:512 , ASP D:96
BINDING SITE FOR RESIDUE NAG C 511
07
AC7
SOFTWARE
TRP C:129 , GLY C:130 , NAG C:511
BINDING SITE FOR RESIDUE NAG C 512
08
AC8
SOFTWARE
TYR A:73 , SER A:76 , PHE A:77 , ARG A:79 , ASP A:80 , LEU A:84 , VAL A:85 , TRP A:133 , ASP A:153 , GLY A:155 , THR A:156
BINDING SITE FOR RESIDUE PBS A 601
09
AC9
SOFTWARE
TYR C:73 , SER C:76 , ASP C:80 , VAL C:85 , TRP C:133 , TRP C:142 , LEU C:143 , LEU C:150 , ASP C:153 , GLY C:155 , THR C:156
BINDING SITE FOR RESIDUE PBS C 602
10
BC1
SOFTWARE
CYS A:12 , GLN A:14 , SER A:28 , PHE A:171
BINDING SITE FOR RESIDUE R16 A 701
11
BC2
SOFTWARE
CYS C:12 , GLN C:14 , SER C:28 , PHE C:70 , ALA C:102
BINDING SITE FOR RESIDUE R16 C 702
[
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SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_B2MG_MOUSE_002 (H34Q, chain B/D, )
2: VAR_B2MG_MOUSE_003 (K44E, chain B/D, )
3: VAR_B2MG_MOUSE_004 (R81T, chain B/D, )
4: VAR_B2MG_MOUSE_005 (A85D, chain B/D, )
5: VAR_B2MG_MOUSE_006 (A85V, chain B/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_B2MG_MOUSE_002
*
H
54
Q
B2MG_MOUSE
---
---
B/D
H
34
Q
2
UniProt
VAR_B2MG_MOUSE_003
*
K
64
E
B2MG_MOUSE
---
---
B/D
K
44
E
3
UniProt
VAR_B2MG_MOUSE_004
*
R
101
T
B2MG_MOUSE
---
---
B/D
R
81
T
4
UniProt
VAR_B2MG_MOUSE_005
*
A
105
D
B2MG_MOUSE
---
---
B/D
A
85
D
5
UniProt
VAR_B2MG_MOUSE_006
*
A
105
V
B2MG_MOUSE
---
---
B/D
A
85
V
* ID not provided by source
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_MOUSE
98-104
2
B:78-84
D:78-84
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1z5la1 (A:186-279)
1b: SCOP_d1z5lc1 (C:186-279)
2a: SCOP_d1z5lb_ (B:)
2b: SCOP_d1z5ld_ (D:)
3a: SCOP_d1z5la2 (A:8-185)
3b: SCOP_d1z5lc2 (C:7-185)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d1z5la1
A:186-279
1b
d1z5lc1
C:186-279
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
beta2-microglobulin
(530)
Mouse (Mus musculus) [TaxId: 10090]
(166)
2a
d1z5lb_
B:
2b
d1z5ld_
D:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
automated matches
(52)
Protein domain
:
automated matches
(52)
Mouse (Mus musculus) [TaxId: 10090]
(29)
3a
d1z5la2
A:8-185
3b
d1z5lc2
C:7-185
[
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1z5lA01 (A:8-184)
1b: CATH_1z5lC01 (C:7-184)
2a: CATH_1z5lB00 (B:2-99)
2b: CATH_1z5lD00 (D:2-99)
2c: CATH_1z5lC02 (C:185-279)
2d: CATH_1z5lA02 (A:185-279)
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)
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)
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(
)
(
)
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)
House mouse (Mus musculus)
(92)
1a
1z5lA01
A:8-184
1b
1z5lC01
C:7-184
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
House mouse (Mus musculus)
(616)
2a
1z5lB00
B:2-99
2b
1z5lD00
D:2-99
2c
1z5lC02
C:185-279
2d
1z5lA02
A:185-279
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_C1_set_1z5lD01 (D:11-92)
1b: PFAM_C1_set_1z5lD02 (D:11-92)
1c: PFAM_C1_set_1z5lC01 (C:194-275)
1d: PFAM_C1_set_1z5lC02 (C:194-275)
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Clans
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Organisms
(
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)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Mus musculus (Mouse)
(118)
1a
C1-set-1z5lD01
D:11-92
1b
C1-set-1z5lD02
D:11-92
1c
C1-set-1z5lC01
C:194-275
1d
C1-set-1z5lC02
C:194-275
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