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Crystal structure of an iron-containing alcohol dehydrogenase (SDEN_2133) from shewanella denitrificans os-217 at 2.12 a resolution

Analyse Crystal structure of an iron-containing alcohol dehydrogenase (SDEN_2133) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RF7
Type: protein
Length: 362 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Iron-containing alcohol dehydrogenase
UniProt: Q12MB1
Ligands: UNL, NAD, CA, FE, NI, CL
Pockets: 1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Iron-containing alcohol dehydrogenase	protein	362	50% helix, 11% strand	Q12MB1

Ligands and binding sites

UNL · Unknown ligand · ligand · chains A
NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
CA · Calcium ion · metal · 2 copies · chains A
FE · Fe (III) ion · metal · chains A
NI · Nickel (II) ion · metal · chains A
CL · Chloride ion · ion · 4 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	528	0.78	0.85	64	UNL, NAD, CL

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

3RF7 · Crystal structure of an Iron-containing alcohol dehydrogenase (Sden_2133) from Shewanella… · 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 Q12MB1
Elsewhere: RCSB PDB 3RF7 · PDBe 3RF7 · UniProt Q12MB1

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