Research workbench
Structure of human mait a-F7 TCR in complex with human MR1-NV18.1
Analyse Structure of human mait a-F7 TCR in complex with human MR1-NV18.1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PVD
- Type
- protein
- Length
- 1,606 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
- N18, NA
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 265 | 29% helix, 40% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C | Major histocompatibility complex class I-related gene protein | protein | 266 | 28% helix, 41% strand | Q95460 |
| D | Human TCR alpha chain | protein | 192 | 2% helix, 48% strand | — |
| E | Human TCR beta chain | protein | 241 | 6% helix, 51% strand | — |
| F | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| G | Human TCR alpha chain | protein | 200 | 5% helix, 45% strand | — |
| H | Human TCR beta chain | protein | 244 | 7% helix, 49% strand | — |
Ligands and binding sites
- N18 · methyl N-(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carbonyl)-beta-alaninate · ligand · 2 copies · chains A, G, C, D
- NA · Sodium ion · metal · chains E
- GOL · Glycerol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.83 | 0.84 | 112 | empty |
| 2 | 425 | 0.76 | 0.85 | 48 | N18 |
| 3 | 330 | 0.75 | 0.86 | 44 | N18 |
| 4 | 1114 | 0.71 | 0.75 | 91 | empty |
| 5 | 943 | 0.69 | 0.75 | 88 | empty |
Interfaces
12 interfaces between chains.
- G–H · 1974 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1944 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1327 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1241 Ų buried · 14 hydrogen bonds · protein-protein
- C–H · 838 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
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 6PVD · PDBe 6PVD · UniProt Q95460 · UniProt P61769
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