Research workbench
Pd-L1 igv domain complex with macro-cyclic peptide
Analyse Pd-L1 igv domain complex with macro-cyclic peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NNV
- Type
- protein
- Length
- 540 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death 1 ligand 1; Macrocyclic peptide
- UniProt
- Q9NZQ7
- Ligands
- ACE, NH2
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death 1 ligand 1 | protein | 119 | 8% helix, 46% strand | Q9NZQ7 |
| B, D | Programmed cell death 1 ligand 1 | protein | 121 | 13% helix, 45% strand | Q9NZQ7 |
| C | Programmed cell death 1 ligand 1 | protein | 123 | 16% helix, 44% strand | Q9NZQ7 |
| I, J, K, L | Macrocyclic peptide | protein | 14 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains B, I, A, J, C, K, D, L
- NH2 · Amino group · ion · 4 copies · chains I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.62 | 0.74 | 65 | ACE, NH2 |
| 2 | 90 | 0.33 | 0.73 | 16 | empty |
| 3 | 67 | 0.31 | 0.75 | 17 | empty |
Interfaces
11 interfaces between chains.
- C–K · 558 Ų buried · 3 hydrogen bonds · protein-protein
- D–L · 548 Ų buried · 4 hydrogen bonds · protein-protein
- A–J · 537 Ų buried · 4 hydrogen bonds · protein-protein
- B–I · 534 Ų buried · 3 hydrogen bonds · protein-protein
- C–I · 350 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 8 covalent, 4 disulfide (nonstandard, covalent ligand, methylation, disulfide).
Compared structures
- 6NNV · PD-L1 IgV domain complex with macro-cyclic peptide · the same entry in another collection · chain A against A, 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 6NNV · PDBe 6NNV · UniProt Q9NZQ7
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