MolNFT v1 · #116117 · protein

Crystal structure of the thioesterase domain of deoxyerythronolide B synthase in complex with a small phosphonate inhibitor

5D3Z · Erythronolide synthase, modules 5 and 6: “Crystal structure of the thioesterase domain of deoxyerythronolide B synthase in complex with a small…”. X-ray diffraction, 2 ligands (57H, CA), 1 pocket (best druggability 0.80). MolNFT v1…

PDB: 5D3Z
Type: protein
Length: 263 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Erythronolide synthase, modules 5 and 6
EC: 2.3.1.94
UniProt: Q03133
Ligands: 57H, CA
Pockets: 1 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Erythronolide synthase, modules 5 and 6 (EC 2.3.1.94)	protein	263	42% helix, 15% strand	Q03133

Ligands and binding sites

57H · prop-2-en-1-ylphosphonic acid · ligand · chains A
CA · Calcium ion · metal · chains A
1PE · Pentaethylene glycol · 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	360	0.80	0.89	44	57H, 1PE

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5D3Z · Crystal structure of the thioesterase domain of deoxyerythronolide B synthase 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 Q03133
Elsewhere: RCSB PDB 5D3Z · PDBe 5D3Z · UniProt Q03133

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