Research workbench
Crystal structure of penicillin-binding protein 5 (PBP5) from pseudomonas aeruginosa in apo state
Analyse Crystal structure of penicillin-binding protein 5 (PBP5) from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K91
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-ala-D-ala-carboxypeptidase
- EC
- 3.4.16.4
- UniProt
- Q02SG6
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-ala-D-ala-carboxypeptidase (EC 3.4.16.4) | protein | 342 | 30% helix, 31% strand | Q02SG6 |
| B | D-ala-D-ala-carboxypeptidase (EC 3.4.16.4) | protein | 342 | 31% helix, 34% strand | Q02SG6 |
Ligands and binding sites
- SIN · Succinic acid · additive · 3 copies · chains A, B
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 | 396 | 0.74 | 0.85 | 50 | SIN |
| 2 | 539 | 0.71 | 0.80 | 48 | SIN |
| 3 | 180 | 0.42 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 631 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4K91 · Crystal structure of Penicillin-Binding Protein 5 (PBP5) from Pseudomonas aeruginosa in… · 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
- Every structure of UniProt Q02SG6
- Elsewhere: RCSB PDB 4K91 · PDBe 4K91 · UniProt Q02SG6
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