MolNFT v1 · #32956 · protein + DNA
The structure of phage PHI29 replication organizer protein P16.7 in complex with double stranded DNA
2C5R · Early protein P16.7: “The structure of phage PHI29 replication organizer protein P16.7 in complex with double stranded DNA”. X-ray diffraction, 3 pockets (best druggability 0.72). MolNFT v1 #32956 on GenesisL1: 3D structure, binding…
- 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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