MolNFT v1 · #61050 · protein
Crystal structure of colicin M, a novel phosphatase specifically imported by escherichia COLI
3DA4 · Colicin-M: “Crystal structure of colicin M, a novel phosphatase specifically imported by escherichia COLI”. X-ray diffraction, 1 ligand (NO3), 4 pockets (best druggability 0.42). MolNFT v1 #61050 on GenesisL1: 3D structure, binding…
- PDB
- 3DA4
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin-M
- UniProt
- P05820
- Ligands
- NO3
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Colicin-M | protein | 270 | 41% helix, 21% strand | P05820 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.42 | 0.74 | 36 | empty |
| 2 | 87 | 0.39 | 0.77 | 18 | empty |
| 3 | 93 | 0.37 | 0.76 | 20 | empty |
| 4 | 59 | 0.31 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 719 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3DA4 · Crystal Structure of Colicin M, a Novel Phosphatase Specifically Imported by Escherichia… · the same entry in another collection · chain A against A, TM-score 1.00
- P05820 · AlphaFold monomer V2.0 prediction for colicin-M (P05820) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P05820
- Elsewhere: RCSB PDB 3DA4 · PDBe 3DA4 · UniProt P05820
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