Research workbench
Rd-1 mart-1 high bound to mart-1 decameric peptide (ela) in complex with HLA-A2
Analyse Rd-1 mart-1 high bound to mart-1 decameric peptide (ela) in complex with HLA-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E9D
- Type
- protein
- Length
- 1,201 residues
- Chains
- 10
- 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; Melanoma…
- UniProt
- P01892, P61769, A0A075B6T6, A0A0K0K1A5
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 8 distinct chains · 14% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 266 | 26% helix, 39% strand | P01892 |
| B, G | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C, H | Melanoma derived mart-1 peptide | protein | 10 | 0% helix, 0% strand | — |
| D | A6-TCR valpha | protein | 110 | 3% helix, 54% strand | A0A075B6T6 |
| E | A6-TCR vbeta | protein | 115 | 5% helix, 53% strand | A0A0K0K1A5 |
| F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 272 | 26% helix, 39% strand | P01892 |
| I | A6-TCR valpha | protein | 108 | 3% helix, 53% strand | A0A075B6T6 |
| J | A6-TCR vbeta | protein | 114 | 5% helix, 52% strand | A0A0K0K1A5 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.69 | 0.96 | 22 | empty |
| 2 | 636 | 0.68 | 0.77 | 62 | empty |
| 3 | 644 | 0.67 | 0.76 | 67 | empty |
| 4 | 160 | 0.63 | 0.85 | 23 | empty |
| 5 | 218 | 0.59 | 0.80 | 40 | empty |
Interfaces
16 interfaces between chains.
- F–G · 1294 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1222 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 901 Ų buried · 13 hydrogen bonds · protein-protein
- F–H · 890 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 707 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5E9D · RD-1 Mart-1 High bound to Mart-1 decameric peptide (ELA) in complex with HLA-A2 · the same entry in another collection · chain J against J, 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 0.99
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 A0A075B6T6
- Every structure of UniProt A0A0K0K1A5
- Elsewhere: RCSB PDB 5E9D · PDBe 5E9D · UniProt P01892 · UniProt P61769 · UniProt A0A075B6T6 · UniProt A0A0K0K1A5
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