MolNFT v1 · #145930 · protein

Crystal structure of corynebacterium diphtheriae udp-galactopyranose mutase in complex with udp-galactopyranose (open, oxidized)

6D2E: “Crystal structure of corynebacterium diphtheriae udp-galactopyranose mutase in complex with…”. X-ray diffraction, 3 ligands (FAD, GDU, NA), 2 pockets (best druggability 0.81). MolNFT v1 #145930 on GenesisL1: 3D structure, binding…

PDB: 6D2E
Type: protein
Length: 386 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-galactopyranose mutase
UniProt: A0A246CDW5
Ligands: FAD, GDU, NA
Pockets: 2 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Udp-galactopyranose mutase	protein	386	39% helix, 19% strand	A0A246CDW5

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
GDU · Galactose-uridine-5'-diphosphate · ligand · chains A
NA · Sodium ion · metal · chains A
IPA · Isopropyl alcohol · 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	1073	0.81	0.82	92	FAD, GDU
2	112	0.40	0.75	21	empty

Compared structures

6D2E · Crystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex… · 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 A0A246CDW5
Elsewhere: RCSB PDB 6D2E · PDBe 6D2E · UniProt A0A246CDW5

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