MolNFT v1 · #15256 · protein
Crystal structures of the nuclease domain of COLE7/IM7 in complex with a phosphate ion and a zinc ion
1MZ8 · Colicin E7 immunity protein: “Crystal structures of the nuclease domain of COLE7/IM7 in complex with a phosphate ion and a zinc ion”. X-ray diffraction, 2 ligands (ZN, PO4), 8 pockets (best druggability 0.69). MolNFT v1 #15256 on…
- PDB
- 1MZ8
- Type
- protein
- Length
- 435 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin E7 immunity protein; Colicin E7
- EC
- 3.1.-.-
- UniProt
- Q03708, Q47112
- Ligands
- ZN, PO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Colicin E7 immunity protein | protein | 87 | 57% helix, 0% strand | Q03708 |
| B | Colicin E7 (EC 3.1.-.-) | protein | 131 | 36% helix, 17% strand | Q47112 |
| D | Colicin E7 (EC 3.1.-.-) | protein | 130 | 36% helix, 17% strand | Q47112 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.69 | 0.79 | 82 | empty |
| 2 | 150 | 0.46 | 0.76 | 24 | empty |
| 3 | 178 | 0.46 | 0.75 | 23 | empty |
| 4 | 161 | 0.43 | 0.74 | 26 | empty |
| 5 | 160 | 0.42 | 0.74 | 27 | ZN, PO4 |
Interfaces
6 interfaces between chains.
- C–D · 796 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 782 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1MZ8 · Crystal structures of the nuclease domain of COLE7/IM7 in complex with a phosphate ion… · the same entry in another collection · chain A against A, TM-score 1.00
- Q03708 · AlphaFold monomer V2.0 prediction for colicin-E7 immunity protein (Q03708) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q47112 · AlphaFold monomer V2.0 prediction for colicin-E7 (Q47112) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q03708
- Every structure of UniProt Q47112
- Elsewhere: RCSB PDB 1MZ8 · PDBe 1MZ8 · UniProt Q03708 · UniProt Q47112
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