MolNFT v1 · #155678 · protein
Crystal structure of vmb-1 bound to hydrolyzed meropenem
6LF4 · Vmb-1 metallo-beta-lactamase: “Crystal structure of vmb-1 bound to hydrolyzed meropenem”. X-ray diffraction, 2 ligands (LMP, ZN), 6 pockets (best druggability 0.79). MolNFT v1 #155678 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6LF4
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vmb-1 metallo-beta-lactamase
- Ligands
- LMP, ZN
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Vmb-1 metallo-beta-lactamase | protein | 219 | 25% helix, 32% strand | — |
Ligands and binding sites
- LMP · (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.79 | 0.83 | 72 | empty |
| 2 | 992 | 0.72 | 0.76 | 74 | ZN, LMP |
| 3 | 388 | 0.62 | 0.77 | 40 | ZN, LMP |
| 4 | 290 | 0.57 | 0.77 | 44 | LMP |
| 5 | 137 | 0.43 | 0.76 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 573 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 517 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 372 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 281 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 179 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6LF4 · Crystal structure of VMB-1 bound to hydrolyzed meropenem · 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
- Elsewhere: RCSB PDB 6LF4 · PDBe 6LF4
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