Research workbench
Photorhabdus virulence cassette (pvc) paar repeat protein PVC10 in complex with a T4 GP5 beta-helix fragment modified to mimic PVC8, the central spike protein of pvc
Analyse Photorhabdus virulence cassette (pvc) paar repeat protein PVC10 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P22
- Type
- protein
- Length
- 419 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of central spike proteins GP5 from phage T4 and PVC8 from pvc; Paar-repeat…
- EC
- 3.2.1.17
- UniProt
- P16009, Q7N647, Q7N648
- Ligands
- STE, ELA, PLM, MG
- Pockets
- 1 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Chimera of central spike proteins GP5 from phage T4 and PVC8 from pvc (EC 3.2.1.17) | protein | 94 | 0% helix, 66% strand | P16009, Q7N647 |
| D | Paar-repeat central spike tip protein | protein | 137 | 4% helix, 53% strand | Q7N648 |
Ligands and binding sites
- STE · Stearic acid · ligand · chains A, B, C
- ELA · 9-octadecenoic acid · ligand · chains A, B, C
- PLM · Palmitic acid · ligand · chains A, B, C
- MG · Magnesium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.85 | 0.86 | 73 | STE, ELA, PLM |
Interfaces
6 interfaces between chains.
- A–C · 3839 Ų buried · 116 hydrogen bonds · protein-protein
- A–B · 3783 Ų buried · 107 hydrogen bonds · protein-protein
- B–C · 3771 Ų buried · 108 hydrogen bonds · protein-protein
- B–D · 348 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 335 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6P22 · Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5… · 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 P16009
- Every structure of UniProt Q7N647
- Every structure of UniProt Q7N648
- Elsewhere: RCSB PDB 6P22 · PDBe 6P22 · UniProt P16009 · UniProt Q7N647 · UniProt Q7N648
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