MolNFT v1 · #166795 · protein
Immune receptor complex
6V13 · HLA class II histocompatibility antigen, dr alpha chain: “Immune receptor complex”. X-ray diffraction, 2 ligands (CIR, NAG), 7 pockets (best druggability 0.71). MolNFT v1 #166795 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6V13
- Type
- protein
- Length
- 814 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
- 7 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 14% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 180 | 18% helix, 44% strand | P13760 |
| C | Fibrinogen beta 74CIT69-81 | protein | 12 | 0% helix, 8% strand | — |
| D | G08 TCR alpha chain | protein | 203 | 4% helix, 44% strand | — |
| E | G08 TCR beta chain | protein | 241 | 7% helix, 50% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.71 | 0.75 | 89 | empty |
| 2 | 254 | 0.70 | 0.85 | 34 | CIR, GOL |
| 3 | 127 | 0.38 | 0.74 | 15 | GOL |
| 4 | 91 | 0.36 | 0.75 | 17 | empty |
| 5 | 52 | 0.33 | 0.78 | 13 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2471 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 2146 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 585 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 534 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 344 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
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 6V13 · PDBe 6V13 · UniProt P01903 · UniProt P13760
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