MolNFT v1 · #31978 · protein
Crystal structure of HLA-A*2402 complexed with a telomerase peptide
2BCK · HLA class I histocompatibility antigen, a-24 alpha chain: “Crystal structure of HLA-A*2402 complexed with a telomerase peptide”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.69). MolNFT v1 #31978 on GenesisL1…
- PDB
- 2BCK
- Type
- protein
- Length
- 790 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-24 alpha chain; Beta-2-microglobulin…
- EC
- 2.7.7.49
- UniProt
- P05534, P61769, O14746
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-24 alpha chain | protein | 286 | 26% helix, 37% strand | P05534 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Telomerase reverse transcriptase (EC 2.7.7.49) | protein | 9 | 0% helix, 0% strand | O14746 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, D, C, B, E
- GOL · Glycerol · additive · 4 copies · chains A, B, D, E
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 | 647 | 0.69 | 0.77 | 53 | GOL |
| 2 | 638 | 0.68 | 0.77 | 57 | GOL |
| 3 | 212 | 0.53 | 0.77 | 31 | SO4 |
| 4 | 160 | 0.51 | 0.79 | 26 | GOL |
| 5 | 196 | 0.50 | 0.76 | 31 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1347 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1322 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 896 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 895 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 587 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2BCK · Crystal Structure of HLA-A*2402 Complexed with a telomerase peptide · 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 E against A, TM-score 0.98
- O14746 · AlphaFold monomer V2.0 prediction for telomerase reverse transcriptase (O14746) · a predicted model of the same protein · chain C against A, TM-score 0.33
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 P05534
- Every structure of UniProt P61769
- Every structure of UniProt O14746
- Elsewhere: RCSB PDB 2BCK · PDBe 2BCK · UniProt P05534 · UniProt P61769 · UniProt O14746
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