MolNFT v1 · #140303 · protein

Vim-2 metallo-beta-lactamase in complex with (R)-2-(4-fluorophenyl)-2- ((S)-3-mercapto-2-METHYLPROPANAMIDO)ACETIC acid (compound 11)

5Y6D · Beta-lactamase class B vim-2: “Vim-2 metallo-beta-lactamase in complex with (R)-2-(4-fluorophenyl)-2…”. X-ray diffraction, 2 ligands (8PL, ZN), 4 pockets (best druggability 0.82). MolNFT v1 #140303 on GenesisL1: 3D structure…

PDB: 5Y6D
Type: protein
Length: 922 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase class B vim-2
UniProt: Q9K2N0
Ligands: 8PL, ZN
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Beta-lactamase class B vim-2	protein	230	28% helix, 29% strand	Q9K2N0
B, C	Beta-lactamase class B vim-2	protein	231	28% helix, 29% strand	Q9K2N0

Ligands and binding sites

8PL · (2R)-2-(4-fluorophenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic acid · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 9 copies · chains A, B, C, D
FMT · Formic acid · additive · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	987	0.82	0.83	108	8PL, ZN
2	93	0.42	0.78	26	empty
3	50	0.41	0.83	15	empty
4	51	0.39	0.81	16	empty

Interfaces

4 interfaces between chains.

A–B · 576 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 530 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 467 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 437 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5Y6D · VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-fluorophenyl)-2-((S)-3-mercapto-2-me… · 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 Q9K2N0
Elsewhere: RCSB PDB 5Y6D · PDBe 5Y6D · UniProt Q9K2N0

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