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Crystal structure of the vim-2 acquired metallo-beta-lactamase in complex with taniborbactam (vnrx-5133)
Analyse Crystal structure of the vim-2 acquired metallo-beta-lactamase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SP7
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase vim-2
- UniProt
- S5M6K4
- Ligands
- K9B, ZN
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Metallo-beta-lactamase vim-2 | protein | 230 | 28% helix, 29% strand | S5M6K4 |
Ligands and binding sites
- K9B · (4~{R})-4-[2-[4-(2-azanylethylamino) cyclohexyl]ethanoylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid · ligand · 2 copies · chains A, E
- ZN · Zinc ion · metal · 6 copies · chains A, E
- ACT · Acetate ion · additive · 4 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.60 | 0.83 | 23 | ZN, K9B |
| 2 | 297 | 0.59 | 0.78 | 26 | empty |
| 3 | 141 | 0.56 | 0.82 | 23 | ZN, K9B |
Interfaces
1 interface between chains.
- A–E · 144 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SP7 · Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in 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 S5M6K4
- Elsewhere: RCSB PDB 6SP7 · PDBe 6SP7 · UniProt S5M6K4
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