Research workbench
Crystal structure of melanoma antigen GP100(209-217) bound to human class I MHC HLA-A2
Analyse Crystal structure of melanoma antigen GP100(209-217) bound to human class I MHC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TVB
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Epitope of…
- UniProt
- P01892, P61769, P40967
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 28% helix, 40% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Epitope of melanocyte protein pmel 17 | protein | 9 | 0% helix, 0% strand | P40967 |
Ligands and binding sites
- GOL · Glycerol · additive · 22 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.78 | 0.80 | 92 | GOL |
| 2 | 661 | 0.69 | 0.78 | 60 | GOL |
| 3 | 154 | 0.53 | 0.80 | 26 | GOL |
| 4 | 155 | 0.50 | 0.78 | 33 | GOL |
| 5 | 139 | 0.48 | 0.78 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1428 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1419 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 872 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 838 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 674 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1TVB · Crystal structure of Melanoma Antigen gp100(209-217) Bound to Human Class I MHC HLA-A2 · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P40967 · AlphaFold monomer V2.0 prediction for melanocyte protein pmel (P40967) · a predicted model of the same protein · chain C against A, TM-score 0.43
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01892
- Every structure of UniProt P61769
- Every structure of UniProt P40967
- Elsewhere: RCSB PDB 1TVB · PDBe 1TVB · UniProt P01892 · UniProt P61769 · UniProt P40967
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