MolNFT v1 · #69410 · protein
Crystal structure of HLA B*4405 in complex with eeylqafty a self peptide from the ABCD3 protein
3KPP · HLA class I histocompatibility antigen, B-44 alpha chain: “Crystal structure of HLA B*4405 in complex with eeylqafty a self peptide from the ABCD3 protein”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #69410 on…
- PDB
- 3KPP
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-44 alpha chain; Beta-2-microglobulin…
- UniProt
- P30481, P61769
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-44 alpha chain | protein | 276 | 28% helix, 39% strand | P30481 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Eeylqafty, self peptide from the ATP binding cassette protein ABCD3 | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.69 | 0.77 | 59 | PEG |
| 2 | 130 | 0.49 | 0.79 | 27 | PEG |
| 3 | 98 | 0.43 | 0.78 | 23 | empty |
| 4 | 59 | 0.38 | 0.80 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1319 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 997 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3KPP · Crystal Structure of HLA B*4405 in complex with EEYLQAFTY a self peptide from the ABCD3… · the same entry in another collection · chain A against A, 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
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 P30481
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3KPP · PDBe 3KPP · UniProt P30481 · UniProt P61769
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