MolNFT v1 · #114297 · protein
High resolution structure of the human pd-1 in complex with pembrolizumab fv
5B8C · Pembrolizumab light chain variable region (pemvl): “High resolution structure of the human pd-1 in complex with pembrolizumab fv”. X-ray diffraction, 12 pockets (best druggability 0.74). MolNFT v1 #114297 on GenesisL1: 3D structure…
- PDB
- 5B8C
- Type
- protein
- Length
- 1,381 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pembrolizumab light chain variable region (pemvl); Pembrolizumab heavy chain variable…
- UniProt
- Q15116
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Pembrolizumab light chain variable region (pemvl) | protein | 111 | 3% helix, 52% strand | — |
| B, H, K | Pembrolizumab heavy chain variable region (pemvh) | protein | 120 | 8% helix, 53% strand | — |
| C, F | Programmed cell death protein 1 | protein | 116 | 3% helix, 52% strand | Q15116 |
| E | Pembrolizumab heavy chain variable region (pemvh) | protein | 119 | 5% helix, 50% strand | — |
| I, L | Programmed cell death protein 1 | protein | 113 | 3% helix, 52% strand | Q15116 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.74 | 0.79 | 100 | empty |
| 2 | 1121 | 0.73 | 0.77 | 108 | empty |
| 3 | 303 | 0.54 | 0.75 | 38 | empty |
| 4 | 129 | 0.50 | 0.80 | 22 | empty |
| 5 | 155 | 0.47 | 0.77 | 32 | empty |
Interfaces
23 interfaces between chains.
- A–B · 807 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 806 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 792 Ų buried · 7 hydrogen bonds · protein-protein
- J–K · 788 Ų buried · 6 hydrogen bonds · protein-protein
- K–L · 736 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5B8C · High resolution structure of the human PD-1 in complex with pembrolizumab Fv · the same entry in another collection · chain L against L, TM-score 1.00
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 Q15116
- Elsewhere: RCSB PDB 5B8C · PDBe 5B8C · UniProt Q15116
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