MolNFT v1 · #93176 · protein
Structure of MHC-class I related molecule MR1
4GUP · Major histocompatibility complex class I-related gene…: “Structure of MHC-class I related molecule MR1”. X-ray diffraction, 3 ligands (6FP, CL, PO4), 13 pockets (best druggability 0.73). MolNFT v1 #93176 on GenesisL1: 3D structure…
- PDB
- 4GUP
- Type
- protein
- Length
- 718 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major histocompatibility complex class I-related gene protein; Beta-2-microglobulin
- UniProt
- Q95460, P61769
- Ligands
- 6FP, CL, PO4
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 265 | 25% helix, 42% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 258 | 25% helix, 40% strand | Q95460 |
| D | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
Ligands and binding sites
- 6FP · 2-amino-4-oxo-3,4-dihydropteridine-6-carbaldehyde · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.73 | 0.95 | 21 | 6FP |
| 2 | 727 | 0.71 | 0.78 | 55 | empty |
| 3 | 226 | 0.68 | 0.84 | 29 | 6FP, CL, PO4 |
| 4 | 565 | 0.66 | 0.76 | 54 | empty |
| 5 | 346 | 0.61 | 0.78 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1179 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1083 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 4GUP · Structure of MHC-class I related molecule MR1 · the same entry in another collection · chain D against D, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q95460 · AlphaFold monomer V2.0 prediction for major histocompatibility complex class I-related… · a predicted model of the same protein · chain C 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 Q95460
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4GUP · PDBe 4GUP · UniProt Q95460 · UniProt P61769
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