MolNFT v1 · #25778 · protein
Crystal structure of PBP4A from bacillus subtilis
1W5D · Penicillin-binding protein: “Crystal structure of PBP4A from bacillus subtilis”. X-ray diffraction, 1 ligand (CA), 1 pocket (best druggability 0.62). MolNFT v1 #25778 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1W5D
- Type
- protein
- Length
- 458 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein
- EC
- 3.4.16.4
- UniProt
- P39844
- Ligands
- CA
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein (EC 3.4.16.4) | protein | 458 | 33% helix, 25% strand | P39844 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.62 | 0.79 | 57 | CA |
Compared structures
- 1W5D · Crystal structure of PBP4a from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P39844 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase dacc (P39844) · a predicted model of the same protein · 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
- Every structure of UniProt P39844
- Elsewhere: RCSB PDB 1W5D · PDBe 1W5D · UniProt P39844
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