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The crystal structure of KanD2 in complex with NAD

Analyse The crystal structure of KanD2 in complex with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JW6
Type: protein
Length: 682 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.8
Source: Streptomyces kanamyceticus
Molecule: Dehydrogenase
EC: 1.1.1.-
UniProt: Q6L737
Ligands: NAD
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · resolution 2.8 · 1 distinct chain · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dehydrogenase (EC 1.1.1.-)	protein	341	38% helix, 24% strand	Q6L737

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

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	646	0.76	0.82	62	NAD
2	650	0.76	0.82	62	NAD
3	253	0.46	0.72	37	empty
4	51	0.39	0.81	25	empty
5	64	0.31	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 1651 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

6JW6 · The crystal structure of KAND2 in complex with NAD · 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 Q6L737
Elsewhere: RCSB PDB 6JW6 · PDBe 6JW6 · UniProt Q6L737

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