Research workbench
Bacteriophage phikz GP163.1 paar repeat protein in complex with the C- terminal part of the T4 GP5 beta-helical domain
Analyse Bacteriophage phikz GP163.1 paar repeat protein in complex with the C- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P1Z
- Type
- protein
- Length
- 726 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baseplate central spike complex protein GP5; Paar-repeat central spike tip protein
- EC
- 3.2.1.17
- UniProt
- P16009, L7T0L4
- Ligands
- PLM, STE, ELA, MG, ZN
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G | Baseplate central spike complex protein GP5 (EC 3.2.1.17) | protein | 92 | 0% helix, 66% strand | P16009 |
| D, H | Paar-repeat central spike tip protein | protein | 87 | 0% helix, 36% strand | L7T0L4 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A, B, C, E, F, G
- STE · Stearic acid · ligand · 2 copies · chains A, B, C, E, F, G
- ELA · 9-octadecenoic acid · ligand · 2 copies · chains A, B, C, E, F, G
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, E, F, G
- ZN · Zinc ion · metal · 2 copies · chains D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.85 | 0.85 | 71 | ELA, PLM, STE |
| 2 | 1084 | 0.84 | 0.85 | 69 | PLM, STE, ELA |
| 3 | 54 | 0.73 | 0.99 | 20 | MG |
Interfaces
12 interfaces between chains.
- F–G · 3735 Ų buried · 119 hydrogen bonds · protein-protein
- B–C · 3729 Ų buried · 114 hydrogen bonds · protein-protein
- E–G · 3725 Ų buried · 111 hydrogen bonds · protein-protein
- E–F · 3717 Ų buried · 110 hydrogen bonds · protein-protein
- A–C · 3715 Ų buried · 105 hydrogen bonds · protein-protein
Compared structures
- 6P1Z · Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with the C-terminal part of… · 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 L7T0L4
- Elsewhere: RCSB PDB 6P1Z · PDBe 6P1Z · UniProt P16009 · UniProt L7T0L4
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