Research workbench
Crystal structure of pseudomonas aeruginosa PBP2 in complex with wck 5153
Analyse Crystal structure of pseudomonas aeruginosa PBP2 in complex with wck 5153 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KIS
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan D,D-transpeptidase mrda
- EC
- 3.4.16.4
- UniProt
- Q9X6V3
- Ligands
- C9D, CL
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase mrda (EC 3.4.16.4) | protein | 458 | 33% helix, 19% strand | Q9X6V3 |
| B | Peptidoglycan D,D-transpeptidase mrda (EC 3.4.16.4) | protein | 440 | 33% helix, 17% strand | Q9X6V3 |
Ligands and binding sites
- C9D · (2S,5R)-1-formyl-N'-[(3R)-pyrrolidine-3-carbonyl]-5-[(sulfooxy)amino]piperidine-2-carbohydrazide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.71 | 0.76 | 81 | empty |
| 2 | 119 | 0.64 | 0.88 | 19 | empty |
| 3 | 271 | 0.54 | 0.76 | 43 | empty |
| 4 | 61 | 0.43 | 0.82 | 18 | empty |
| 5 | 106 | 0.41 | 0.77 | 21 | C9D |
Interfaces
1 interface between chains.
- A–B · 586 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7KIS · Crystal structure of Pseudomonas aeruginosa PBP2 in complex with WCK 5153 · 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 Q9X6V3
- Elsewhere: RCSB PDB 7KIS · PDBe 7KIS · UniProt Q9X6V3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.