MolNFT v1 · #164258 · protein
Human leukocyte antigen class I A02 carrying llwngpmqv
6SSA · HLA class I histocompatibility antigen, a-2 alpha chain: “Human leukocyte antigen class I A02 carrying llwngpmqv”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.77). MolNFT v1 #164258 on GenesisL1: 3D structure…
- PDB
- 6SSA
- Type
- protein
- Length
- 1,540 residues
- Chains
- 12
- 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
- CA
- Pockets
- 20 · 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, G, J | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 39% strand | P01892 |
| B, E, H, K | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F, I, L | Leu-leu-TRP-asn-gly-pro-met-gln-val | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains K
- GOL · Glycerol · additive · 12 copies · chains A, B, D, E, G, H, J, K
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains B, D, G, H, J
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, G, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.77 | 0.81 | 68 | PEG |
| 2 | 997 | 0.77 | 0.79 | 77 | GOL |
| 3 | 786 | 0.72 | 0.78 | 82 | empty |
| 4 | 690 | 0.70 | 0.77 | 65 | empty |
| 5 | 447 | 0.68 | 0.79 | 39 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1326 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1311 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 1310 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1294 Ų buried · 14 hydrogen bonds · protein-protein
- G–I · 913 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6SSA · Human Leukocyte Antigen Class I A02 Carrying LLWNGPMQV · the same entry in another collection · chain L against L, 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6SSA · PDBe 6SSA · UniProt P01892 · UniProt P61769
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