MolNFT v1 · #103521 · protein
Structure of human MR1-5-op-ru in complex with human mait TRBV20 TCR
4PJ8 · Major histocompatibility complex class I-related gene…: “Structure of human MR1-5-op-ru in complex with human mait TRBV20 TCR”. X-ray diffraction, 2 ligands (2LJ, NA), 9 pockets (best druggability 0.77). MolNFT v1 #103521 on…
- PDB
- 4PJ8
- Type
- protein
- Length
- 797 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
- 2LJ, NA
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 260 | 28% helix, 42% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 48% strand | P61769 |
| C | TCR-alpha | protein | 197 | 2% helix, 49% strand | — |
| D | TCR-beta | protein | 243 | 7% helix, 48% strand | — |
Ligands and binding sites
- 2LJ · 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol · ligand · chains A, C, D
- NA · Sodium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.77 | 0.83 | 68 | empty |
| 2 | 97 | 0.77 | 0.97 | 23 | 2LJ |
| 3 | 1012 | 0.69 | 0.74 | 105 | empty |
| 4 | 513 | 0.63 | 0.76 | 53 | empty |
| 5 | 232 | 0.50 | 0.75 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1884 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1204 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 686 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 501 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4PJ8 · Structure of human MR1-5-OP-RU in complex with human MAIT TRBV20 TCR · the same entry in another collection · chain A against A, TM-score 1.00
- Q95460 · AlphaFold monomer V2.0 prediction for major histocompatibility complex class I-related… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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
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 4PJ8 · PDBe 4PJ8 · UniProt Q95460 · UniProt P61769
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