MolNFT v1 · #17805 · protein
Crystal structure of weissella viridescens FEMX:UDP-murnac- pentapeptide complex
1P4N: “Crystal structure of weissella viridescens FEMX:UDP-murnac- pentapeptide complex”. X-ray diffraction, 3 ligands (UMA, FGA, MG), 3 pockets (best druggability 0.69). MolNFT v1 #17805 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1P4N
- Type
- protein
- Length
- 338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Femx; Udp-murnac-pentapeptide
- EC
- 2.3.2.10
- Ligands
- UMA, FGA, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Femx (EC 2.3.2.10) | protein | 335 | 37% helix, 27% strand | — |
| B | Udp-murnac-pentapeptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- UMA · Uridine-5'-diphosphate-N-acetylmuramoyl-L-alanine · ligand · chains A, B
- FGA · Gamma-D-glutamic acid · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.69 | 0.77 | 57 | FGA, GOL |
| 2 | 132 | 0.57 | 0.83 | 24 | empty |
| 3 | 236 | 0.52 | 0.76 | 31 | UMA |
Interfaces
1 interface between chains.
- A–B · 222 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 d-amino, 1 covalent (D-amino acid, covalent ligand).
Compared structures
- 1P4N · Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentapeptide complex · 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 1P4N · PDBe 1P4N
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