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Crystal structure of malus domestica double bond reductase (mddbr) apo form

Analyse Crystal structure of malus domestica double bond reductase (mddbr) apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YSB
Type: protein
Length: 678 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-alkenal reductase (NADP(+)-dependent)-like
Ligands: SO4
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	2-alkenal reductase (NADP(+)-dependent)-like	protein	339	33% helix, 28% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B, A

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

Pockets

9 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	632	0.80	0.85	64	SO4
2	652	0.80	0.84	61	SO4
3	113	0.33	0.72	21	empty
4	56	0.33	0.76	11	empty
5	69	0.32	0.75	11	empty

Interfaces

1 interface between chains.

B–A · 280 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6YSB · Crystal structure of Malus domestica Double Bond Reductase (MdDBR) apo form · the same entry in another collection · chain B against B, 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 6YSB · PDBe 6YSB

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