MolNFT v1 · #100198 · protein
Crystal structure of comj, inhibitor of the DNA degrading activity of nuca, from bacillus subtilis
4MQD · DNA-entry nuclease inhibitor: “Crystal structure of comj, inhibitor of the DNA degrading activity of nuca, from bacillus subtilis”. X-ray diffraction, 7 pockets (best druggability 0.77). MolNFT v1 #100198 on GenesisL1: 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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