Research workbench
HLA-E*01:03 in complex with the MTB44 peptide variant: MTB44*P2-gln.
Analyse HLA-E*01:03 in complex with the MTB44 peptide variant: MTB44*P2-gln. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GH4
- Type
- protein
- Length
- 1,531 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Arg-gln-pro-ala-lys-ala-pro-leu-leu
- UniProt
- E2G051, P61769
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | MHC class I antigen | protein | 274 | 27% helix, 39% strand | E2G051 |
| B, D, F, H | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| E | MHC class I antigen | protein | 273 | 27% helix, 40% strand | E2G051 |
| P, Q, R, Y | Arg-gln-pro-ala-lys-ala-pro-leu-leu | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 600 | 0.77 | 0.83 | 77 | empty |
| 2 | 1153 | 0.72 | 0.76 | 84 | empty |
| 3 | 526 | 0.66 | 0.77 | 53 | empty |
| 4 | 298 | 0.59 | 0.78 | 40 | empty |
| 5 | 137 | 0.53 | 0.81 | 24 | empty |
Interfaces
15 interfaces between chains.
- G–H · 1456 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1390 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1384 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1357 Ų buried · 19 hydrogen bonds · protein-protein
- G–Y · 896 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6GH4 · HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln. · the same entry in another collection · chain Y against Y, TM-score 1.00
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 E2G051
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6GH4 · PDBe 6GH4 · UniProt E2G051 · UniProt P61769
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