5WLG
Crystal Structure of H-2Db with the GAP501 peptide (SQL)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, F (A, F) | H-2 class I histocompatibility antigen, D-B alpha chain | polymer | 278 | 32281.9 | 2 | UniProt (P01899) Pfam (PF00129) Pfam (PF07654) | Mus musculus (Mouse) | H-2D(B) |
| 2 | B, G (B, G) | Beta-2-microglobulin | polymer | 99 | 11660.4 | 2 | UniProt (P01887) Pfam (PF07654) | Mus musculus (Mouse) | |
| 3 | C, H (C, H) | GAP50 peptide | polymer | 9 | 1050.2 | 2 | UniProt (A0A0Y9W4B5) | Plasmodium berghei | |
| 4 | D, I (D, I) | T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain | polymer | 182 | 20203.3 | 2 | UniProt (A0A075B616) UniProt (K7N5M3) Pfam (PF07686) Pfam (PF09291) | Mus musculus (Mouse) | Human nkt tcr beta chain |
| 5 | E, J (E, J) | T-cell receptor beta chain V region C5,Human nkt tcr beta chain | polymer | 243 | 27303.1 | 2 | UniProt (P04213) UniProt (K7N5M4) Pfam (PF07686) Pfam (PF07654) | Mus musculus (Mouse) | |
| 6 | K, M, N (A, G, I) | SODIUM ION | non-polymer | 23.0 | 3 | Chemie (NA) | |||
| 7 | L (A) | CHLORIDE ION | non-polymer | 35.5 | 1 | Chemie (CL) | |||
| 8 | O, P, Q, R, S... (A, B, C, D, E...) | water | water | 18.0 | 890 | Chemie (HOH) |
Sequence modifications
D, I: 5 - 90 (UniProt: A0A075B616)
D, I: 110 - 186 (UniProt: K7N5M3)
E, J: 1 - 113 (UniProt: P04213)
E, J: 114 - 243 (UniProt: K7N5M4)
| PDB | External Database | Details |
|---|---|---|
| Val 91 | - | linker |
| Tyr 92 | - | linker |
| Ala 93 | - | linker |
| Gln 94 | - | linker |
| Gly 95 | - | linker |
| Leu 96 | - | linker |
| Thr 97 | - | linker |
| Phe 98 | - | linker |
| Gly 99 | - | linker |
| Leu 100 | - | linker |
| Gly 101 | - | linker |
| Thr 102 | - | linker |
| Arg 103 | - | linker |
| Val 104 | - | linker |
| Ser 105 | - | linker |
| Val 106 | - | linker |
| Phe 107 | - | linker |
| Pro 108 | - | linker |
| Asn 109 | - | linker |
E, J: 1 - 113 (UniProt: P04213)
| PDB | External Database | Details |
|---|---|---|
| Asp 95 | Gly 103 | conflict |
| Trp 96 | Thr 104 | conflict |
| - | Gly 106 | deletion |
| - | Ala 107 | deletion |
| - | Leu 108 | deletion |
| Gly 100 | - | insertion |
| Leu 102 | - | insertion |
| Glu 106 | Pro 115 | conflict |
| Ser 108 | Thr 117 | conflict |
| Lys 109 | Arg 118 | conflict |
| Thr 111 | Leu 120 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 10 |
| Total formula weight | 184998.0 | |
| Non-Polymers* | Number of molecules | 4 |
| Total formula weight | 104.4 | |
| All* | Total formula weight | 185102.4 |
