MolNFT v1 · #166800 · protein
Immune receptor complex
6V18 · HLA class II histocompatibility antigen, dr alpha chain: “Immune receptor complex”. X-ray diffraction, 2 ligands (CIR, NAG), 10 pockets (best druggability 0.75). MolNFT v1 #166800 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6V18
- Type
- protein
- Length
- 817 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P13760
- Ligands
- CIR, NAG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 14% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 178 | 19% helix, 43% strand | P13760 |
| C | Fibrinogen beta | protein | 12 | 0% helix, 8% strand | — |
| D | M141 TCR alpha chain | protein | 206 | 3% helix, 47% strand | — |
| E | M141 TCR beta chain | protein | 242 | 7% helix, 52% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 13 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.75 | 0.97 | 21 | CIR |
| 2 | 1096 | 0.72 | 0.76 | 78 | GOL |
| 3 | 150 | 0.46 | 0.76 | 25 | empty |
| 4 | 174 | 0.45 | 0.75 | 38 | GOL |
| 5 | 92 | 0.42 | 0.78 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2511 Ų buried · 48 hydrogen bonds · protein-protein
- D–E · 2332 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 590 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 400 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
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 P01903
- Every structure of UniProt P13760
- Elsewhere: RCSB PDB 6V18 · PDBe 6V18 · UniProt P01903 · UniProt P13760
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