MolNFT v1 · #57834 · protein

Crystal structure of NADH-dependent quinuclidinone reductase from agrobacterium tumefaciens

3AK4: “Crystal structure of NADH-dependent quinuclidinone reductase from agrobacterium tumefaciens”. X-ray diffraction, 1 ligand (NAD), 8 pockets (best druggability 0.86). MolNFT v1 #57834 on GenesisL1: 3D structure, binding sites and…

PDB: 3AK4
Type: protein
Length: 1,032 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADH-dependent quinuclidinone reductase
Ligands: NAD
Pockets: 8 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	NADH-dependent quinuclidinone reductase	protein	258	52% helix, 14% strand	—

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1026	0.86	0.87	110	NAD
2	1025	0.86	0.86	115	NAD
3	235	0.82	0.94	32	empty
4	106	0.43	0.77	19	empty
5	93	0.41	0.77	19	empty

Interfaces

6 interfaces between chains.

A–B · 1827 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1774 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 1612 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1596 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 85 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3AK4 · Crystal structure of NADH-dependent quinuclidi reductase from agrobacterium tumefaciens · 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 3AK4 · PDBe 3AK4

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