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Crystal structure of the dimeric form of repe in complex with the repe operator DNA
Analyse Crystal structure of the dimeric form of repe in complex with the repe operator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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