MolNFT v1 · #159819 · protein
Bacteriophage phikz GP163.1 paar repeat protein in complex with a T4 GP5 beta-helix fragment modified to mimic the phikz central spike GP164
6P20 · Baseplate central spike complex protein GP5,PHIKZ164: “Bacteriophage phikz GP163.1 paar repeat protein in complex with a T4 GP5 beta-helix fragment modified to…”. X-ray diffraction, 5 ligands (STE, ELA, PLM), 2 pockets (best…
- PDB
- 6P20
- Type
- protein
- Length
- 415 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baseplate central spike complex protein GP5,PHIKZ164; Paar-repeat central spike tip…
- EC
- 3.2.1.17
- UniProt
- P16009, Q8SCZ8, L7T0L4
- Ligands
- STE, ELA, PLM, MG, ZN
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baseplate central spike complex protein GP5,PHIKZ164 (EC 3.2.1.17) | protein | 110 | 0% helix, 63% strand | P16009, Q8SCZ8 |
| B, C | Baseplate central spike complex protein GP5,PHIKZ164 (EC 3.2.1.17) | protein | 109 | 0% helix, 63% strand | P16009, Q8SCZ8 |
| D | Paar-repeat central spike tip protein | protein | 87 | 0% helix, 34% strand | L7T0L4 |
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 · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · chains D
- EDO · 1,2-ethanediol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.85 | 0.85 | 71 | STE, ELA, PLM |
| 2 | 94 | 0.79 | 0.99 | 20 | MG |
Interfaces
6 interfaces between chains.
- B–C · 4535 Ų buried · 131 hydrogen bonds · protein-protein
- A–B · 4498 Ų buried · 132 hydrogen bonds · protein-protein
- A–C · 4428 Ų buried · 135 hydrogen bonds · protein-protein
- C–D · 373 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 340 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6P20 · Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with a T4 gp5 beta-helix… · 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 Q8SCZ8
- Every structure of UniProt L7T0L4
- Elsewhere: RCSB PDB 6P20 · PDBe 6P20 · UniProt P16009 · UniProt Q8SCZ8 · UniProt L7T0L4
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