MolNFT v1 · #115919 · protein
Structure of the PONA1 protein from mycobacterium tuberculosis in complex with penicillin V
5CXW · Penicillin-binding protein 1A: “Structure of the PONA1 protein from mycobacterium tuberculosis in complex with penicillin V”. X-ray diffraction, 1 ligand (35P), 2 pockets (best druggability 0.63). MolNFT v1 #115919 on GenesisL1: 3D…
- PDB
- 5CXW
- Type
- protein
- Length
- 376 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1A
- UniProt
- P71707
- Ligands
- 35P
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1A | protein | 376 | 36% helix, 22% strand | P71707 |
Ligands and binding sites
- 35P · (2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenoxyacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.63 | 0.79 | 42 | 35P |
| 2 | 81 | 0.35 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5CXW · Structure of the PonA1 protein from Mycobacterium Tuberculosis in complex with penicillin… · the same entry in another collection · chain A against A, TM-score 1.00
- P71707 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 1A (P71707) · 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 P71707
- Elsewhere: RCSB PDB 5CXW · PDBe 5CXW · UniProt P71707
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