MolNFT v1 · #141924 · protein
Colicin D central domain and C-terminal trnase domain
5ZNM · Colicin-D: “Colicin D central domain and C-terminal trnase domain”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.79). MolNFT v1 #141924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZNM
- Type
- protein
- Length
- 715 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin-D
- UniProt
- P17998
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colicin-D | protein | 358 | 24% helix, 29% strand | P17998 |
| B | Colicin-D | protein | 357 | 23% helix, 30% strand | P17998 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.79 | 0.83 | 63 | GOL |
| 2 | 259 | 0.64 | 0.82 | 42 | SO4 |
| 3 | 303 | 0.62 | 0.79 | 49 | SO4 |
| 4 | 328 | 0.59 | 0.77 | 55 | empty |
| 5 | 181 | 0.58 | 0.82 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1736 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
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 P17998
- Elsewhere: RCSB PDB 5ZNM · PDBe 5ZNM · UniProt P17998
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