MolNFT v1 · #175713 · protein
Crystal structure of pd-L1 in complex with a vhh
7CZD · Anti-pd-L1 vhh: “Crystal structure of pd-L1 in complex with a vhh”. X-ray diffraction, 3 pockets (best druggability 0.36). MolNFT v1 #175713 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CZD
- Type
- protein
- Length
- 464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-pd-L1 vhh; Programmed cell death 1 ligand 1
- UniProt
- Q9NZQ7
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-pd-L1 vhh | protein | 116 | 8% helix, 47% strand | — |
| B, D | Programmed cell death 1 ligand 1 | protein | 117 | 11% helix, 48% strand | Q9NZQ7 |
| C | Anti-pd-L1 vhh | protein | 114 | 8% helix, 47% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.36 | 0.77 | 16 | empty |
| 2 | 67 | 0.30 | 0.74 | 15 | empty |
| 3 | 52 | 0.27 | 0.75 | 11 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 878 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 867 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 517 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7CZD · Crystal structure of PD-L1 in complex with a VHH · the same entry in another collection · chain B against B, 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 Q9NZQ7
- Elsewhere: RCSB PDB 7CZD · PDBe 7CZD · UniProt Q9NZQ7
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