Research workbench
The structure of phage PHI29 replication organizer protein P16.7 in complex with double stranded DNA
Analyse The structure of phage PHI29 replication organizer protein P16.7 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C5R
- Type
- protein + DNA
- Length
- 394 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Early protein P16.7; 5'-D(*TP*CP*CP*AP*CP*CP*GP*GP)-3'; 5'-D(*CP*CP*GP*GP*TP*GP*GP*AP)-3'
- UniProt
- P16517
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Early protein P16.7 | protein | 63 | 60% helix, 0% strand | P16517 |
| Y | 5'-D(*TP*CP*CP*AP*CP*CP*GP*GP)-3' | dna | 8 | — | — |
| Z | 5'-D(*CP*CP*GP*GP*TP*GP*GP*AP)-3' | dna | 8 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.72 | 0.77 | 58 | empty |
| 2 | 91 | 0.38 | 0.76 | 19 | empty |
| 3 | 57 | 0.33 | 0.77 | 17 | empty |
Interfaces
21 interfaces between chains.
- E–F · 1406 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1392 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1329 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 641 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 638 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2C5R · The structure of phage phi29 replication organizer protein p16.7 in complex with double… · 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 P16517
- Elsewhere: RCSB PDB 2C5R · PDBe 2C5R · UniProt P16517
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