MolNFT v1 · #128920 · protein
Structure of human pd-L1 in complex with inhibitor
5O4Y · Programmed cell death 1 ligand 1: “Structure of human pd-L1 in complex with inhibitor”. X-ray diffraction, 1 ligand (NH2), 2 pockets (best druggability 0.65). MolNFT v1 #128920 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5O4Y
- Type
- protein
- Length
- 399 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death 1 ligand 1; Phe-maa-asn-pro-his-leu-ser-TRP-ser-TRP-9KK-9KK-arg-ccs…
- UniProt
- Q9NZQ7
- Ligands
- NH2
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, E | Programmed cell death 1 ligand 1 | protein | 118 | 13% helix, 45% strand | Q9NZQ7 |
| A, D, F | Phe-maa-asn-pro-his-leu-ser-TRP-ser-TRP-9KK-9KK-arg-ccs- gly-NH2 | protein | 15 | 0% helix, 13% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 3 copies · chains A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.65 | 0.79 | 49 | empty |
| 2 | 67 | 0.30 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–D · 588 Ų buried · 8 hydrogen bonds · protein-protein
- E–A · 586 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 570 Ų buried · 3 hydrogen bonds · protein-protein
- E–D · 305 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 290 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 3 disulfide (nonstandard, disulfide).
Compared structures
- 5O4Y · Structure of human PD-L1 in complex with inhibitor · 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 5O4Y · PDBe 5O4Y · UniProt Q9NZQ7
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