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Crystal structure of a short chain dehydrogenase in complex with NAD(P) from sinorhizobium meliloti 1021

Analyse Crystal structure of a short chain dehydrogenase in complex with NAD(P) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TOX
Type: protein
Length: 2,023 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short chain dehydrogenase
UniProt: Q92SS3
Ligands: NAP
Pockets: 17 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, I	Short chain dehydrogenase	protein	254	47% helix, 15% strand	Q92SS3
B	Short chain dehydrogenase	protein	248	48% helix, 17% strand	Q92SS3
F	Short chain dehydrogenase	protein	254	46% helix, 16% strand	Q92SS3
G	Short chain dehydrogenase	protein	251	48% helix, 16% strand	Q92SS3

Ligands and binding sites

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

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

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	704	0.85	0.89	75	empty
2	484	0.76	0.84	49	NAP
3	464	0.75	0.84	49	NAP
4	365	0.75	0.86	43	NAP
5	371	0.75	0.86	43	NAP

Interfaces

10 interfaces between chains.

D–I · 1685 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1683 Å² buried · 22 hydrogen bonds · protein-protein
D–F · 1394 Å² buried · 11 hydrogen bonds · protein-protein
E–I · 1347 Å² buried · 11 hydrogen bonds · protein-protein
F–I · 482 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3TOX · Crystal structure of a short chain dehydrogenase in complex with NAD(P) 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 Q92SS3
Elsewhere: RCSB PDB 3TOX · PDBe 3TOX · UniProt Q92SS3

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