MolNFT v1 · #114966 · protein

Crystal structure of NADP-dependent dehydrogenase from rhodobacter sphaeroides

5C5I: “Crystal structure of NADP-dependent dehydrogenase from rhodobacter sphaeroides”. X-ray diffraction, 6 pockets (best druggability 0.75). MolNFT v1 #114966 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5C5I
Type: protein
Length: 620 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADP-dependent dehydrogenase
EC: 1.1.1.79, 1.1.1.81
UniProt: Q3IWN8
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NADP-dependent dehydrogenase (EC 1.1.1.79, 1.1.1.81)	protein	311	41% helix, 18% strand	Q3IWN8
B	NADP-dependent dehydrogenase (EC 1.1.1.79, 1.1.1.81)	protein	309	42% helix, 18% strand	Q3IWN8

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	527	0.75	0.83	65	empty
2	103	0.74	0.95	26	empty
3	428	0.67	0.79	47	empty
4	244	0.63	0.81	39	empty
5	109	0.46	0.79	21	empty

Interfaces

1 interface between chains.

A–B · 2433 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

5C5I · Crystal structure of NADP-dependent dehydrogenase from Rhodobacter sphaeroides · 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 Q3IWN8
Elsewhere: RCSB PDB 5C5I · PDBe 5C5I · UniProt Q3IWN8

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