5VCJ
Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Antigen-presenting glycoprotein CD1d1 | polymer | 285 | 32632.7 | 1 | UniProt (P11609) Pfam (PF16497) Pfam (PF07654) | Mus musculus (Mouse) | |
| 2 | B (B) | Beta-2-microglobulin | polymer | 99 | 11660.4 | 1 | UniProt (P01887) Pfam (PF07654) | Mus musculus (Mouse) | |
| 3 | C (C) | Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain) | polymer | 209 | 23055.6 | 1 | UniProt (A0A0B4J1J9) UniProt (K7N5M3) Pfam (PF07686) Pfam (PF09291) | Mus musculus (Mouse) | T cell receptor alpha variable 11D,Human nkt tcr beta chain |
| 4 | D (D) | Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain) | polymer | 241 | 27027.0 | 1 | Mus musculus (Mouse) | ||
| 5 | E (E) | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1057.0 | 1 | In PDB GlyTouCan (G82348BZ) | |||
| 6 | F (A) | (2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside | non-polymer | 479.6 | 1 | Chemie (N57) | |||
| 7 | G (A) | PALMITIC ACID | non-polymer | 256.4 | 1 | Chemie (PLM) | |||
| 8 | H, I (A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 2 | Chemie (NAG) |
Sequence modifications
A: 1 - 279 (UniProt: P11609)
C: 1 - 93 (UniProt: A0A0B4J1J9)
C: 114 - 208 (UniProt: K7N5M3)
D: 0 - 129 (PDB: 5VCJ)
D: 130 - 240 (PDB: 5VCJ)
| PDB | External Database | Details |
|---|---|---|
| His 201 | Asp 219 | engineered mutation |
| His 280 | - | expression tag |
| His 281 | - | expression tag |
| His 282 | - | expression tag |
| His 283 | - | expression tag |
| His 284 | - | expression tag |
| His 285 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Met 0 | - | initiating methionine |
| Asp 94 | - | linker |
| Arg 95 | - | linker |
| Gly 96 | - | linker |
| Ser 97 | - | linker |
| Ala 98 | - | linker |
| Leu 99 | - | linker |
| Gly 100 | - | linker |
| Arg 101 | - | linker |
| Leu 102 | - | linker |
| His 103 | - | linker |
| Phe 104 | - | linker |
| Gly 105 | - | linker |
| Ala 106 | - | linker |
| Gly 107 | - | linker |
| Thr 108 | - | linker |
| Gln 109 | - | linker |
| Leu 110 | - | linker |
| Ile 111 | - | linker |
| Val 112 | - | linker |
| Ile 113 | - | linker |
D: 0 - 129 (PDB: 5VCJ)
D: 130 - 240 (PDB: 5VCJ)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 4 |
| Total formula weight | 94375.6 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 1057.0 | |
| Non-Polymers* | Number of molecules | 4 |
| Total formula weight | 1178.5 | |
| All* | Total formula weight | 96611.1 |
