Research workbench
HLA-E*01:03 in complex with the MTB44 peptide variant: MTB44*P9-phe.
Analyse HLA-E*01:03 in complex with the MTB44 peptide variant: MTB44*P9-phe. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GHN
- Type
- protein
- Length
- 759 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, E alpha chain variant; Beta-2-microglobulin…
- UniProt
- Q59EE1, P61769
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, E alpha chain variant | protein | 269 | 26% helix, 39% strand | Q59EE1 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | HLA class I histocompatibility antigen, E alpha chain variant | protein | 272 | 26% helix, 40% strand | Q59EE1 |
| P, Q | Arg-leu-pro-ala-lys-ala-pro-leu-phe | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.72 | 0.76 | 106 | empty |
| 2 | 668 | 0.69 | 0.77 | 58 | empty |
| 3 | 673 | 0.69 | 0.77 | 58 | empty |
| 4 | 54 | 0.58 | 0.91 | 15 | empty |
| 5 | 92 | 0.53 | 0.84 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1368 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1354 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 898 Ų buried · 9 hydrogen bonds · protein-protein
- C–Q · 887 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 318 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6GHN · HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P9-Phe. · the same entry in another collection · chain Q against Q, 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 Q59EE1
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6GHN · PDBe 6GHN · UniProt Q59EE1 · UniProt P61769
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