Research workbench
Crystal structure of the receptor binding protein (GP15) of listeria phage psa
Analyse Crystal structure of the receptor binding protein (GP15) of listeria phage psa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R5W
- Type
- protein
- Length
- 508 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP15 protein
- UniProt
- Q8W5Z4
- Ligands
- CD
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GP15 protein | protein | 171 | 26% helix, 37% strand | Q8W5Z4 |
| B | GP15 protein | protein | 168 | 26% helix, 37% strand | Q8W5Z4 |
| C | GP15 protein | protein | 169 | 26% helix, 37% strand | Q8W5Z4 |
Ligands and binding sites
- CD · Cadmium ion · metal · 9 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains 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 | 61 | 0.69 | 0.96 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2335 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2322 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2258 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6R5W · Crystal structure of the receptor binding protein (gp15) of Listeria phage PSA · 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 Q8W5Z4
- Elsewhere: RCSB PDB 6R5W · PDBe 6R5W · UniProt Q8W5Z4
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