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Crystal structure of a putative NAD(P) dependent gluconate 5- dehydrogenase from beutenbergia CAVERNAE(EFI target efi-502044) with bound NADP (low occupancy)

Analyse Crystal structure of a putative NAD(P) dependent gluconate 5- dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3UF0
Type: protein
Length: 498 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short-chain DEHYDROGENASE/REDUCTASE sdr
EC: 1.1.1.125
UniProt: C5BY10
Ligands: NAP
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Short-chain DEHYDROGENASE/REDUCTASE sdr (EC 1.1.1.125)	protein	249	52% helix, 16% strand	C5BY10

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B

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

Pockets

2 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	360	0.72	0.84	46	NAP
2	408	0.72	0.83	58	NAP

Interfaces

1 interface between chains.

A–B · 1602 Å² buried · 37 hydrogen bonds · protein-protein

Compared structures

3UF0 · Crystal structure of a putative NAD(P) dependent gluconate 5-dehydrogenase from… · 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 C5BY10
Elsewhere: RCSB PDB 3UF0 · PDBe 3UF0 · UniProt C5BY10

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