MolNFT v1 · #136047 · protein
1.95 ångström resolution crystal structure of fragment (35-274) of membrane-bound lytic murein transglycosylase F from yersinia pestis.
5UH0: “1.95 ångström resolution crystal structure of fragment (35-274) of membrane-bound lytic murein…”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.79). MolNFT v1 #136047 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5UH0
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-bound lytic murein transglycosylase F
- EC
- 4.2.2.-
- UniProt
- Q74SQ6
- Ligands
- CL
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 233 | 37% helix, 27% strand | Q74SQ6 |
| B | Membrane-bound lytic murein transglycosylase F (EC 4.2.2.-) | protein | 228 | 39% helix, 27% strand | Q74SQ6 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.79 | 0.98 | 31 | CL |
| 2 | 121 | 0.79 | 0.97 | 33 | CL |
| 3 | 830 | 0.72 | 0.77 | 70 | empty |
| 4 | 58 | 0.26 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 432 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 5UH0 · 1.95 Angstrom Resolution Crystal Structure of Fragment (35-274) of Membrane-bound Lytic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q74SQ6 · AlphaFold monomer V2.0 prediction for membrane-bound lytic murein transglycosylase F… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q74SQ6
- Elsewhere: RCSB PDB 5UH0 · PDBe 5UH0 · UniProt Q74SQ6
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