MolNFT v1 · #56259 · protein + DNA
Crystal structure of the dimeric form of repe in complex with the repe operator DNA
2Z9O · Replication initiation protein: “Crystal structure of the dimeric form of repe in complex with the repe operator DNA”. X-ray diffraction, 6 pockets (best druggability 0.65). MolNFT v1 #56259 on GenesisL1: 3D structure, binding sites…
- PDB
- 2Z9O
- Type
- protein + DNA
- Length
- 506 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication initiation protein; DNA (33-mer)
- UniProt
- P03856
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication initiation protein | protein | 222 | 44% helix, 22% strand | P03856 |
| B | Replication initiation protein | protein | 218 | 45% helix, 23% strand | P03856 |
| C | DNA (33-mer) | dna | 33 | — | — |
| D | DNA (33-mer) | dna | 33 | — | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.65 | 0.74 | 53 | empty |
| 2 | 492 | 0.59 | 0.74 | 42 | empty |
| 3 | 129 | 0.41 | 0.75 | 18 | empty |
| 4 | 77 | 0.38 | 0.77 | 16 | empty |
| 5 | 56 | 0.31 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1414 Ų buried · 132 hydrogen bonds · nucleic-nucleic
- A–B · 1347 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 487 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 470 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 414 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2Z9O · Crystal structure of the dimeric form of RepE in complex with the repE operator DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P03856 · AlphaFold monomer V2.0 prediction for replication initiation protein (P03856) · a predicted model of the same protein · chain A against A, TM-score 0.60
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 P03856
- Elsewhere: RCSB PDB 2Z9O · PDBe 2Z9O · UniProt P03856
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