Research workbench
Crystal structure of HLA_DRB1*04:01 in complex with alpha-enolase peptide 26-40
Analyse Crystal structure of HLA_DRB1*04:01 in complex with alpha-enolase peptide 26-40 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LAX
- Type
- protein
- Length
- 769 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P13760
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 181 | 15% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 193 | 19% helix, 44% strand | P13760 |
| C | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 15% helix, 46% strand | P01903 |
| D | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 188 | 19% helix, 45% strand | P13760 |
| E, F | Alpha-enolase peptidetskglfraavpsgas | protein | 14 | 0% helix, 14% strand | — |
Ligands and binding sites
- MLA · Malonic acid · additive · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.68 | 0.82 | 43 | empty |
| 2 | 162 | 0.61 | 0.84 | 25 | empty |
| 3 | 92 | 0.52 | 0.83 | 25 | empty |
| 4 | 110 | 0.52 | 0.82 | 24 | empty |
| 5 | 108 | 0.48 | 0.81 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2583 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2536 Ų buried · 44 hydrogen bonds · protein-protein
- A–E · 640 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 626 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 602 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5LAX · Crystal structure of HLA_DRB1*04:01 in complex with alpha-enolase peptide 26-40 · the same entry in another collection · chain F against F, TM-score 1.00
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P01903
- Every structure of UniProt P13760
- Elsewhere: RCSB PDB 5LAX · PDBe 5LAX · UniProt P01903 · UniProt P13760
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.