Research workbench
HLA-E*01:03 in complex with IL9
Analyse HLA-E*01:03 in complex with IL9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P4B
- Type
- protein
- Length
- 1,524 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, alpha chain E; Beta-2-microglobulin; Esat-6-like…
- UniProt
- P13747, P61769, P9WNK3
- Ligands
- ZN, SO4, PO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | HLA class I histocompatibility antigen, alpha chain E | protein | 276 | 27% helix, 39% strand | P13747 |
| B, D, F, H | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| E | HLA class I histocompatibility antigen, alpha chain E | protein | 260 | 25% helix, 35% strand | P13747 |
| P, Q, R, Z | Esat-6-like protein esxh | protein | 9 | 0% helix, 0% strand | P9WNK3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains E, G
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, E, C, D, Q, F, G, H
- PO4 · Phosphate ion · ion
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.77 | 0.79 | 76 | GOL |
| 2 | 677 | 0.71 | 0.78 | 59 | SO4 |
| 3 | 56 | 0.69 | 0.97 | 18 | empty |
| 4 | 662 | 0.68 | 0.77 | 63 | GOL, SO4 |
| 5 | 609 | 0.68 | 0.77 | 59 | GOL |
Interfaces
18 interfaces between chains.
- C–D · 1402 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1384 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1377 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1336 Ų buried · 22 hydrogen bonds · protein-protein
- A–P · 898 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7P4B · HLA-E*01:03 in complex with IL9 · the same entry in another collection · chain Z against Z, 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 P13747
- Every structure of UniProt P61769
- Every structure of UniProt P9WNK3
- Elsewhere: RCSB PDB 7P4B · PDBe 7P4B · UniProt P13747 · UniProt P61769 · UniProt P9WNK3
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