MolNFT v1 · #167650 · protein
Structure of a pseudomurein peptide ligase type E from methanothermus fervidus
6VR8 · Mur ligase middle domain protein: “Structure of a pseudomurein peptide ligase type E from methanothermus fervidus”. X-ray diffraction, 4 ligands (UDP, MG, SO4), 3 pockets (best druggability 0.67). MolNFT v1 #167650 on GenesisL1: 3D…
- PDB
- 6VR8
- Type
- protein
- Length
- 482 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mur ligase middle domain protein
- EC
- 6.3.2.-
- UniProt
- E3GZ29
- Ligands
- UDP, MG, SO4, PO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Mur ligase middle domain protein (EC 6.3.2.-) | protein | 482 | 39% helix, 22% strand | E3GZ29 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains I
- MG · Magnesium ion · metal · chains I
- SO4 · Sulfate ion · ion · 3 copies · chains I
- PO4 · Phosphate ion · ion · chains I
- EDO · 1,2-ethanediol · additive · 2 copies · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.67 | 0.79 | 54 | PO4, MG, SO4 |
| 2 | 293 | 0.56 | 0.76 | 36 | empty |
| 3 | 50 | 0.27 | 0.74 | 10 | UDP |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6VR8 · Structure of a pseudomurein peptide ligase type E from Methanothermus fervidus · the same entry in another collection · chain I against I, 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
- Every structure of UniProt E3GZ29
- Elsewhere: RCSB PDB 6VR8 · PDBe 6VR8 · UniProt E3GZ29
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