MolNFT v1 · #166801 · protein
Immune receptor complex
6V19 · HLA class II histocompatibility antigen, dr alpha chain: “Immune receptor complex”. X-ray diffraction, 2 ligands (CIR, NAG), 11 pockets (best druggability 0.71). MolNFT v1 #166801 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6V19
- Type
- protein
- Length
- 813 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
- 11 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 177 | 13% helix, 48% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 178 | 17% helix, 39% strand | P13760 |
| C | Fibrinogen beta 72,74CIT69-81 | protein | 11 | 0% helix, 9% strand | — |
| D | M134 TCR alpha chain | protein | 205 | 3% helix, 45% strand | — |
| E | M134 TCR beta chain | protein | 242 | 7% helix, 51% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · 2 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.71 | 0.75 | 79 | GOL |
| 2 | 222 | 0.71 | 0.87 | 42 | CIR, GOL |
| 3 | 92 | 0.46 | 0.81 | 21 | empty |
| 4 | 130 | 0.41 | 0.75 | 23 | empty |
| 5 | 55 | 0.35 | 0.79 | 15 | GOL |
Interfaces
10 interfaces between chains.
- A–B · 2342 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 2279 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 533 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 516 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 380 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 5 covalent, 1 glycan (disulfide, covalent ligand, additive adduct, 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 6V19 · PDBe 6V19 · UniProt P01903 · UniProt P13760
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