MolNFT v1 · #109520 · protein
Structure of the class D beta-lactamase oxa-225 K82D in acyl-enzyme complex with ceftazidime
4X55: “Structure of the class D beta-lactamase oxa-225 K82D in acyl-enzyme complex with ceftazidime”. X-ray diffraction, 1 ligand (CTJ), 3 pockets (best druggability 0.42). MolNFT v1 #109520 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4X55
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase oxa-225
- UniProt
- G5DE28
- Ligands
- CTJ
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase oxa-225 | protein | 243 | 40% helix, 23% strand | G5DE28 |
| B | Beta-lactamase oxa-225 | protein | 232 | 41% helix, 22% strand | G5DE28 |
Ligands and binding sites
- CTJ · 1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium · ligand · 2 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.42 | 0.73 | 27 | CTJ |
| 2 | 98 | 0.32 | 0.72 | 16 | CTJ |
| 3 | 51 | 0.31 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 503 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4X55 · Structure of the class D Beta-Lactamase OXA-225 K82D in Acyl-Enzyme Complex with… · 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 G5DE28
- Elsewhere: RCSB PDB 4X55 · PDBe 4X55 · UniProt G5DE28
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