MolNFT v1 · #71050 · protein
Crystal structure of fluorescein-labeled class a -lactamase penp
3M2J · Beta-lactamase: “Crystal structure of fluorescein-labeled class a -lactamase penp”. X-ray diffraction, 2 ligands (F5M, SO4), 5 pockets (best druggability 0.74). MolNFT v1 #71050 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3M2J
- 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
- P00808
- Ligands
- F5M, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 256 | 43% helix, 18% strand | P00808 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 257 | 42% helix, 17% strand | P00808 |
Ligands and binding sites
- F5M · 5-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 1127 | 0.74 | 0.77 | 91 | empty |
| 2 | 82 | 0.46 | 0.81 | 18 | empty |
| 3 | 65 | 0.44 | 0.82 | 19 | empty |
| 4 | 71 | 0.34 | 0.76 | 21 | SO4, F5M |
| 5 | 70 | 0.29 | 0.73 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 553 Ų buried · 4 hydrogen bonds · protein-protein
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 P00808
- Elsewhere: RCSB PDB 3M2J · PDBe 3M2J · UniProt P00808
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