MolNFT v1 · #83620 · protein

Crystal structure of yidc from bacillus halodurans (form I)

3WO6 · Membrane protein insertase yidc 2: “Crystal structure of yidc from bacillus halodurans (form I)”. X-ray diffraction, 1 ligand (CD), 2 pockets (best druggability 0.61). MolNFT v1 #83620 on GenesisL1: 3D structure, binding sites and…

PDB: 3WO6
Type: protein
Length: 212 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Membrane protein insertase yidc 2
UniProt: Q9KDP2
Ligands: CD
Pockets: 2 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Membrane protein insertase yidc 2	protein	212	77% helix, 2% strand	Q9KDP2

Ligands and binding sites

CD · Cadmium ion · metal · chains A
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	373	0.61	0.77	34	empty
2	71	0.47	0.82	13	empty

Compared structures

3WO6 · Crystal structure of YidC from Bacillus halodurans (form I) · the same entry in another collection · chain A against A, TM-score 1.00
Q9KDP2 · AlphaFold monomer V2.0 prediction for membrane protein insertase yidc 2 (Q9KDP2) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 Q9KDP2
Elsewhere: RCSB PDB 3WO6 · PDBe 3WO6 · UniProt Q9KDP2

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