MolNFT v1 · #99760 · protein
Immune receptor
4MD4 · HLA class II histocompatibility antigen, dr alpha chain: “Immune receptor”. X-ray diffraction, 2 ligands (CIR, NAG), 3 pockets (best druggability 0.52). MolNFT v1 #99760 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MD4
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- 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, P16112
- Ligands
- CIR, NAG
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 182 | 13% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 189 | 19% helix, 46% strand | P13760 |
| C | Aggrecan core protein | protein | 11 | 0% helix, 9% strand | P16112 |
Ligands and binding sites
- CIR · Citrulline · ligand · 2 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.52 | 0.76 | 25 | EDO |
| 2 | 155 | 0.43 | 0.75 | 24 | EDO |
| 3 | 60 | 0.35 | 0.78 | 18 | CIR |
Interfaces
3 interfaces between chains.
- A–B · 2614 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 607 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 564 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 3 disulfide, 3 glycan (covalent ligand, disulfide, N-glycosylation).
Compared structures
- 4MD4 · Immune Receptor · 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
- P16112 · AlphaFold monomer V2.0 prediction for aggrecan core protein (P16112) · a predicted model of the same protein · chain C against A, TM-score 0.43
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
- Every structure of UniProt P16112
- Elsewhere: RCSB PDB 4MD4 · PDBe 4MD4 · UniProt P01903 · UniProt P13760 · UniProt P16112
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