MolNFT v1 · #118185 · protein
Crystal structure of extended-spectrum beta-lactamase bel-1 in complex with moxalactam
5EUA: “Crystal structure of extended-spectrum beta-lactamase bel-1 in complex with moxalactam”. X-ray diffraction, 2 ligands (3P7, NA), 4 pockets (best druggability 0.70). MolNFT v1 #118185 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5EUA
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q3SAW3
- Ligands
- 3P7, NA
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 263 | 46% helix, 19% strand | Q3SAW3 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 250 | 45% helix, 20% strand | Q3SAW3 |
Ligands and binding sites
- 3P7 · (2R)-2-[(1R)-1-{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}-1-methoxy-2-oxoethyl]-5-methylidene-5,6-dihydro-2H-1,3 -oxazine-4-carboxylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.70 | 0.79 | 61 | empty |
| 2 | 80 | 0.40 | 0.79 | 18 | empty |
| 3 | 66 | 0.37 | 0.78 | 15 | empty |
| 4 | 65 | 0.28 | 0.73 | 20 | 3P7 |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 5EUA · Crystal structure of extended-spectrum beta-lactamase BEL-1 in complex with Moxalactam · 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 Q3SAW3
- Elsewhere: RCSB PDB 5EUA · PDBe 5EUA · UniProt Q3SAW3
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