MolNFT v1 · #144081 · protein
HLA-DRB1 in complex with type II collagen peptide
6BIN · HLA class II histocompatibility antigen, dr alpha chain: “HLA-DRB1 in complex with type II collagen peptide”. X-ray diffraction, 2 ligands (CIR, NAG), 2 pockets (best druggability 0.43). MolNFT v1 #144081 on GenesisL1: 3D structure…
- PDB
- 6BIN
- Type
- protein
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; Type II collagen 1240CIT…
- UniProt
- P01903, P13760
- Ligands
- CIR, NAG
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 13% helix, 47% strand | P01903 |
| C | Type II collagen 1240CIT 1237-1249 | protein | 12 | 0% helix, 8% strand | — |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 189 | 17% helix, 44% strand | P13760 |
Ligands and binding sites
- CIR · Citrulline · ligand · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.43 | 0.75 | 20 | empty |
| 2 | 110 | 0.40 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2514 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 529 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6BIN · HLA-DRB1 in complex with Type II collagen peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 6BIN · PDBe 6BIN · UniProt P01903 · UniProt P13760
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