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Crystal structure of the kpc-2 carbapenemase

Analyse Crystal structure of the kpc-2 carbapenemase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OV5
Type: protein
Length: 783 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carbapenemase
EC: 3.5.2.6
UniProt: Q93LQ9
Ligands: BCN
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Carbapenemase (EC 3.5.2.6)	protein	261	43% helix, 17% strand	Q93LQ9

Ligands and binding sites

BCN · Bicine · ligand · 3 copies · chains A, B, C

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	404	0.64	0.79	52	empty
2	468	0.64	0.77	57	empty
3	70	0.33	0.75	11	empty
4	86	0.33	0.74	15	BCN
5	72	0.30	0.74	17	BCN

Interfaces

2 interfaces between chains.

B–C · 382 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 225 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

2OV5 · Crystal structure of the KPC-2 carbapenemase · 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 Q93LQ9
Elsewhere: RCSB PDB 2OV5 · PDBe 2OV5 · UniProt Q93LQ9

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