MolNFT v1 · #150146 · protein
HLA-E*01:03 in complex with the HIV epitope, RL9HIV
6GL1 · MHC class I antigen: “HLA-E*01:03 in complex with the HIV epitope, RL9HIV”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #150146 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GL1
- Type
- protein
- Length
- 1,506 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Arg-met-tyr-ser-pro-thr-ser-ile-leu
- UniProt
- E2G051, P61769
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | MHC class I antigen | protein | 274 | 27% helix, 39% strand | E2G051 |
| B, D, F, H | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C | MHC class I antigen | protein | 273 | 27% helix, 40% strand | E2G051 |
| G | MHC class I antigen | protein | 249 | 28% helix, 34% strand | E2G051 |
| P, R, T, Q | Arg-met-tyr-ser-pro-thr-ser-ile-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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.80 | 0.81 | 105 | empty |
| 2 | 1190 | 0.77 | 0.79 | 107 | empty |
| 3 | 492 | 0.70 | 0.80 | 53 | empty |
| 4 | 478 | 0.68 | 0.79 | 51 | empty |
| 5 | 602 | 0.67 | 0.77 | 57 | empty |
Interfaces
21 interfaces between chains.
- C–D · 1405 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1382 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1381 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1372 Ų buried · 22 hydrogen bonds · protein-protein
- E–R · 946 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6GL1 · HLA-E*01:03 in complex with the HIV epitope, RL9HIV · the same entry in another collection · chain Q against Q, 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 6GL1 · PDBe 6GL1 · UniProt E2G051 · UniProt P61769
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