MolNFT v1 · #176481 · protein

Crystal structure of azotobacter vinelandii L-rhamnose 1- DEHYDROGENASE(NADP bound-form)

7DO6 · Short-chain DEHYDROGENASE/REDUCTASE sdr: “Crystal structure of azotobacter vinelandii L-rhamnose 1- DEHYDROGENASE(NADP bound-form)”. X-ray diffraction, 1 ligand (NAP), 20 pockets (best druggability 0.87). MolNFT v1 #176481 on…

PDB: 7DO6
Type: protein
Length: 1,994 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short-chain DEHYDROGENASE/REDUCTASE sdr
UniProt: C1DMX5
Ligands: NAP
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, H	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	247	49% helix, 17% strand	C1DMX5
B	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	247	46% helix, 17% strand	C1DMX5
C, D	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	256	48% helix, 16% strand	C1DMX5
F	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	246	48% helix, 17% strand	C1DMX5
G	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	248	47% helix, 17% strand	C1DMX5

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	777	0.87	0.89	63	empty
2	776	0.86	0.89	62	empty
3	1160	0.83	0.84	96	empty
4	602	0.76	0.82	71	NAP
5	656	0.72	0.79	63	NAP

Interfaces

15 interfaces between chains.

E–F · 1797 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1770 Å² buried · 34 hydrogen bonds · protein-protein
G–H · 1762 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1753 Å² buried · 31 hydrogen bonds · protein-protein
E–H · 1591 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

7DO6 · Crystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrogenase(NADP bound-form) · 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 C1DMX5
Elsewhere: RCSB PDB 7DO6 · PDBe 7DO6 · UniProt C1DMX5

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