Research workbench
Crystal structure of comj, inhibitor of the DNA degrading activity of nuca, from bacillus subtilis
Analyse Crystal structure of comj, inhibitor of the DNA degrading activity of nuca… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MQD
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-entry nuclease inhibitor
- UniProt
- P12669
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA-entry nuclease inhibitor | protein | 133 | 5% helix, 49% strand | P12669 |
| B, C | DNA-entry nuclease inhibitor | protein | 132 | 5% helix, 50% strand | P12669 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.77 | 0.79 | 97 | empty |
| 2 | 185 | 0.52 | 0.78 | 21 | empty |
| 3 | 182 | 0.51 | 0.78 | 21 | empty |
| 4 | 81 | 0.35 | 0.75 | 15 | empty |
| 5 | 79 | 0.34 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 482 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 461 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 382 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 378 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 283 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4MQD · Crystal structure of ComJ, inhibitor of the DNA degrading activity of NucA, from Bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- P12669 · AlphaFold monomer V2.0 prediction for DNA-entry nuclease inhibitor (P12669) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P12669
- Elsewhere: RCSB PDB 4MQD · PDBe 4MQD · UniProt P12669
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