Research workbench
Structure of human MR1-5-op-ru in complex with human mait B-F3-C1 TCR
Analyse Structure of human MR1-5-op-ru in complex with human mait B-F3-C1 TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PJB
- Type
- protein
- Length
- 1,569 residues
- Chains
- 8
- 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
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 264 | 28% helix, 41% strand | Q95460 |
| B, D | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 260 | 28% helix, 43% strand | Q95460 |
| E | TCR-alpha | protein | 188 | 4% helix, 48% strand | — |
| F | TCR-beta | protein | 230 | 6% helix, 49% strand | — |
| G | TCR-alpha | protein | 197 | 4% helix, 46% strand | — |
| H | TCR-beta | protein | 238 | 6% 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 · 2 copies · chains A, E, C, G
- GOL · Glycerol · additive · 3 copies · chains B, C, A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.77 | 0.84 | 61 | 2LJ |
| 2 | 460 | 0.77 | 0.85 | 60 | 2LJ |
| 3 | 761 | 0.74 | 0.79 | 64 | GOL |
| 4 | 1011 | 0.71 | 0.75 | 85 | empty |
| 5 | 956 | 0.71 | 0.75 | 74 | empty |
Interfaces
11 interfaces between chains.
- G–H · 1968 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1787 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1171 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1168 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 707 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 4PJB · Structure of human MR1-5-OP-RU in complex with human MAIT B-F3-C1 TCR · the same entry in another collection · chain H against H, 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 C against A, TM-score 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D 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 4PJB · PDBe 4PJB · UniProt Q95460 · UniProt P61769
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