Research workbench
HLA-E*01:03 in complex with the MTB44 peptide variant: MTB44*P2-phe.
Analyse HLA-E*01:03 in complex with the MTB44 peptide variant: MTB44*P2-phe. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GGM
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; MTB44*P2-phe peptide variant…
- UniProt
- E2G051, P61769
- Ligands
- ZN, SO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 274 | 27% helix, 38% strand | E2G051 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | MHC class I antigen | protein | 270 | 27% helix, 39% strand | E2G051 |
| P, Q | MTB44*P2-phe peptide variant (arg-phe-pro-ala-lys-ala-pro- leu-leu) | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C, P
- SO4 · Sulfate ion · ion · 6 copies · chains A, P, B, D, C
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 | 383 | 0.75 | 0.86 | 51 | SO4 |
| 2 | 297 | 0.73 | 0.86 | 45 | empty |
| 3 | 78 | 0.52 | 0.85 | 17 | empty |
| 4 | 158 | 0.51 | 0.79 | 26 | empty |
| 5 | 79 | 0.48 | 0.83 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1394 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1379 Ų buried · 25 hydrogen bonds · protein-protein
- A–P · 935 Ų buried · 10 hydrogen bonds · protein-protein
- C–Q · 926 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 507 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6GGM · HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-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 E2G051
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6GGM · PDBe 6GGM · UniProt E2G051 · UniProt P61769
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