MolNFT v1 · #19510 · protein
Penicillin-binding protein 2X (pbp-2X) acyl-enzyme complex
1QMF: “Penicillin-binding protein 2X (pbp-2X) acyl-enzyme complex”. X-ray diffraction, 2 ligands (CES, KEF), 5 pockets (best druggability 0.72). MolNFT v1 #19510 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1QMF
- Type
- protein
- Length
- 559 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2X
- UniProt
- P14677
- Ligands
- CES, KEF
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2X | protein | 559 | 27% helix, 25% strand | P14677 |
Ligands and binding sites
- CES · 2-[carboxy-(2-furan-2-yl-2-methoxyimino-acetylamino)-methyl]-5-methyl-3,6-dihydro-2H-[1,3]thiazine-4-carboxylic acid · ligand · chains A
- KEF · Cefuroxime (oct-3-ene form) · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.72 | 0.84 | 42 | KEF |
| 2 | 476 | 0.67 | 0.79 | 48 | CES |
| 3 | 111 | 0.41 | 0.76 | 15 | empty |
| 4 | 63 | 0.35 | 0.78 | 15 | empty |
| 5 | 57 | 0.33 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 P14677
- Elsewhere: RCSB PDB 1QMF · PDBe 1QMF · UniProt P14677
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