MolNFT v1 · #99756 · protein
Immune receptor
4MCZ · HLA class II histocompatibility antigen, dr alpha chain: “Immune receptor”. X-ray diffraction, 2 ligands (CIR, NAG), 4 pockets (best druggability 0.43). MolNFT v1 #99756 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MCZ
- 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; HLA class II histocompatibility…
- UniProt
- P01903, P13760, P08670
- Ligands
- CIR, NAG
- Pockets
- 4 · best druggability 0.43
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 | 179 | 13% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 189 | 19% helix, 46% strand | P13760 |
| C | Citrullinated vimentin | protein | 12 | 0% helix, 8% strand | P08670 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.43 | 0.73 | 20 | empty |
| 2 | 125 | 0.41 | 0.76 | 20 | empty |
| 3 | 51 | 0.38 | 0.81 | 13 | CIR |
| 4 | 53 | 0.28 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2486 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 635 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 605 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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
- Every structure of UniProt P08670
- Elsewhere: RCSB PDB 4MCZ · PDBe 4MCZ · UniProt P01903 · UniProt P13760 · UniProt P08670
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