Research workbench
Structural basis for the inhibition of E. COLI PBP2
Analyse Structural basis for the inhibition of E. COLI PBP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G9F
- Type
- protein
- Length
- 539 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan D,D-transpeptidase mrda
- EC
- 3.4.16.4
- UniProt
- P0AD65
- Ligands
- NXL
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase mrda (EC 3.4.16.4) | protein | 539 | 37% helix, 23% strand | P0AD65 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.63 | 0.77 | 49 | empty |
| 2 | 152 | 0.43 | 0.75 | 29 | NXL |
| 3 | 125 | 0.42 | 0.76 | 20 | empty |
| 4 | 63 | 0.36 | 0.78 | 13 | empty |
| 5 | 55 | 0.30 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6G9F · Structural basis for the inhibition of E. coli PBP2 · the same entry in another collection · chain A against A, TM-score 1.00
- P0AD65 · AlphaFold monomer V2.0 prediction for peptidoglycan D,D-transpeptidase mrda (P0AD65) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0AD65
- Elsewhere: RCSB PDB 6G9F · PDBe 6G9F · UniProt P0AD65
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