Research workbench
Structure of human D462-E4 TCR in complex with human MR1-5-op-ru
Analyse Structure of human D462-E4 TCR in complex with human MR1-5-op-ru in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XQP
- Type
- protein
- Length
- 1,576 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, NA, CL, BR
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 14% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 243 | 30% helix, 38% strand | Q95460 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 254 | 29% helix, 39% strand | Q95460 |
| E | TRAV12-2 alpha chain | protein | 193 | 3% helix, 49% strand | — |
| F, H | TRBV29-1 | protein | 246 | 6% helix, 50% strand | — |
| G | TRAV12-2 alpha chain | protein | 194 | 2% helix, 45% 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, C, H
- NA · Sodium ion · metal · chains D, F
- CL · Chloride ion · ion · 4 copies · chains A, F, E, C, H, G
- BR · Bromide ion · ion · 2 copies · chains A, E, C, G
- GOL · Glycerol · additive · 7 copies · chains A, F, C, E, H, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.83 | 0.96 | 40 | 2LJ |
| 2 | 182 | 0.82 | 0.97 | 38 | 2LJ |
| 3 | 921 | 0.75 | 0.78 | 78 | GOL |
| 4 | 397 | 0.73 | 0.84 | 41 | GOL |
| 5 | 1026 | 0.73 | 0.76 | 82 | empty |
Interfaces
14 interfaces between chains.
- G–H · 1972 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1889 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1382 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1333 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 729 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 covalent (disulfide, 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 Q95460
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6XQP · PDBe 6XQP · UniProt Q95460 · UniProt P61769
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