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Crystal structure of corynebacterium glutamicum pimb' bound to GDP-man (orthorhombic crystal form)

Analyse Crystal structure of corynebacterium glutamicum pimb' bound to GDP-man… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OKP
Type: protein
Length: 378 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
EC: 2.4.1.57
UniProt: Q8NNK8
Ligands: GDD
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase (EC 2.4.1.57)	protein	378	48% helix, 16% strand	Q8NNK8

Ligands and binding sites

GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 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	601	0.67	0.77	58	GDD
2	68	0.31	0.75	16	empty

Compared structures

3OKP · Crystal structure of Corynebacterium glutamicum PimB' bound to GDP-Man (orthorhombic… · the same entry in another collection · chain A against A, TM-score 1.00
Q8NNK8 · AlphaFold monomer V2.0 prediction for GDP-mannose-dependent monoacylated… · a predicted model of the same protein · chain A against A, TM-score 0.98

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8NNK8
Elsewhere: RCSB PDB 3OKP · PDBe 3OKP · UniProt Q8NNK8

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