Research workbench
Crystal structure of pectocin M2 at 1.86 ångströms
Analyse Crystal structure of pectocin M2 at 1.86 ångströms in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N58
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectocin M2
- Ligands
- FES, SO4, CL
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectocin M2 | protein | 266 | 29% helix, 30% strand | — |
| B | Pectocin M2 | protein | 266 | 30% helix, 30% strand | — |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 18 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 35 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.60 | 0.77 | 42 | SO4, GOL |
| 2 | 232 | 0.52 | 0.76 | 31 | SO4, GOL, MPD |
| 3 | 59 | 0.36 | 0.78 | 13 | GOL |
| 4 | 100 | 0.35 | 0.73 | 18 | MPD |
| 5 | 85 | 0.34 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 309 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4N58 · Crystal Structure of Pectocin M2 at 1.86 Angstroms · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4N58 · PDBe 4N58
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