MolNFT v1 · #142793 · protein
Crystal structure of class a B-lactamase, penl, variant ASN136ASP, from burkholderia thailandensis, in complex with ceftazidime-like boronic acid
6AFP · Beta-lactamase: “Crystal structure of class a B-lactamase, penl, variant ASN136ASP, from burkholderia thailandensis, in…”. X-ray diffraction, 1 ligand (CB4), 3 pockets (best druggability 0.73). MolNFT v1 #142793 on GenesisL1: 3D…
- PDB
- 6AFP
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A2Z4SUB5
- Ligands
- CB4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 268 | 44% helix, 21% strand | A0A2Z4SUB5 |
Ligands and binding sites
- CB4 · Pinacol[[2-amino-alpha-(1-carboxy-1-methylethoxyimino)-4-thiazoleacetyl]amino]methaneboronate · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.73 | 0.76 | 99 | empty |
| 2 | 73 | 0.33 | 0.76 | 21 | CB4 |
| 3 | 89 | 0.32 | 0.74 | 18 | CB4 |
Interfaces
1 interface between chains.
- A–B · 610 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6AFP · Crystal structure of class A b-lactamase, PenL, variant Asn136Asp, from Burkholderia… · 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 A0A2Z4SUB5
- Elsewhere: RCSB PDB 6AFP · PDBe 6AFP · UniProt A0A2Z4SUB5
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