Research workbench
Structure of human MR1-5-op-ru in complex with human mait TRAJ20 TCR
Analyse Structure of human MR1-5-op-ru in complex with human mait TRAJ20 TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PJ9
- Type
- protein
- Length
- 780 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
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 262 | 28% helix, 42% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C | TCR-alpha | protein | 190 | 5% helix, 48% strand | — |
| D | TCR-beta | protein | 230 | 8% helix, 50% 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
- NA · Sodium ion · metal · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.76 | 0.86 | 44 | 2LJ |
| 2 | 954 | 0.70 | 0.75 | 85 | empty |
| 3 | 500 | 0.63 | 0.76 | 54 | GOL |
| 4 | 207 | 0.53 | 0.78 | 23 | GOL |
| 5 | 252 | 0.53 | 0.76 | 35 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1944 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1219 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 670 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 519 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4PJ9 · Structure of human MR1-5-OP-RU in complex with human MAIT TRAJ20 TCR · the same entry in another collection · chain A against A, 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 0.98
- 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
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 4PJ9 · PDBe 4PJ9 · UniProt Q95460 · UniProt P61769
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