Research workbench
Human leukocyte antigen class I A02 carrying llwngpiav
Analyse Human leukocyte antigen class I A02 carrying llwngpiav in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SS8
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61769
- Ligands
- P4G, SO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 27% helix, 39% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Leu-leu-TRP-asn-gly-pro-ile-ala-val | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · chains D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, D, F, E
- GOL · Glycerol · additive · 9 copies · chains A, D, B, E
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.77 | 0.79 | 87 | GOL, SO4 |
| 2 | 693 | 0.70 | 0.78 | 68 | SO4 |
| 3 | 603 | 0.68 | 0.77 | 56 | PEG |
| 4 | 174 | 0.59 | 0.83 | 22 | empty |
| 5 | 136 | 0.45 | 0.77 | 19 | GOL, PEG |
Interfaces
7 interfaces between chains.
- A–B · 1376 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1355 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 870 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 844 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 395 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6SS8 · PDBe 6SS8 · UniProt P01892 · UniProt P61769
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