MolNFT v1 · #153031 · protein
Complex structure of gy-5 Fab and pd-1
6J15 · Programmed cell death protein 1: “Complex structure of gy-5 Fab and pd-1”. X-ray diffraction, 3 ligands (NAG, FUC, MAN), 7 pockets (best druggability 0.69). MolNFT v1 #153031 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6J15
- Type
- protein
- Length
- 1,056 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 1; Gy-5 heavy chain Fab; Gy-5 light chain Fab
- UniProt
- Q15116
- Ligands
- NAG, FUC, MAN
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Programmed cell death protein 1 | protein | 110 | 3% helix, 57% strand | Q15116 |
| D | Programmed cell death protein 1 | protein | 106 | 3% helix, 57% strand | Q15116 |
| H | Gy-5 heavy chain Fab | protein | 203 | 4% helix, 54% strand | — |
| L, B | Gy-5 light chain Fab | protein | 216 | 6% helix, 51% strand | — |
| A | Gy-5 heavy chain Fab | protein | 205 | 4% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C, D
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.69 | 0.80 | 68 | empty |
| 2 | 403 | 0.58 | 0.75 | 50 | empty |
| 3 | 407 | 0.57 | 0.74 | 60 | empty |
| 4 | 151 | 0.44 | 0.76 | 21 | empty |
| 5 | 121 | 0.36 | 0.73 | 18 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1860 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1832 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 583 Ų buried · 13 hydrogen bonds · protein-protein
- C–A · 568 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 553 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
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 Q15116
- Elsewhere: RCSB PDB 6J15 · PDBe 6J15 · UniProt Q15116
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