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Crystal Structure of NDM-1 D199N with Compound 16

Analyse Crystal Structure of NDM-1 D199N with Compound 16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NY7
Type: protein
Length: 229 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.4
Source: Klebsiella pneumoniae
Molecule: Carbapenem Hydrolyzing Class B Metallo beta lactamase NDM-1
EC: 3.5.2.6
UniProt: E9NWK5
Ligands: L8J, ZN
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · resolution 1.4 · 1 distinct chain · 27% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Carbapenem Hydrolyzing Class B Metallo beta lactamase NDM-1 (EC 3.5.2.6)	protein	229	27% helix, 31% strand	E9NWK5

Ligands and binding sites

L8J · [(5,7-dibromo-2-oxo-1,2-dihydroquinolin-4-yl) methyl]phosphonic acid · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.35	0.74	22	ZN, L8J

Compared structures

6NY7 · Crystal structure of ndm-1 D199N with compound 16 · 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 E9NWK5
Elsewhere: RCSB PDB 6NY7 · PDBe 6NY7 · UniProt E9NWK5

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