MolNFT v1 · #94701 · protein

The structure of SGCE10, the acp-polyene thioesterase involved in C- 1027 biosynthesis

4I4J: “The structure of SGCE10, the acp-polyene thioesterase involved in C- 1027 biosynthesis”. X-ray diffraction, 11 pockets (best druggability 0.86). MolNFT v1 #94701 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4I4J
Type: protein
Length: 1,119 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acp-polyene thioesterase
UniProt: Q8GME8
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 26% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Acp-polyene thioesterase	protein	140	24% helix, 42% strand	Q8GME8
D	Acp-polyene thioesterase	protein	136	24% helix, 41% strand	Q8GME8
E	Acp-polyene thioesterase	protein	138	26% helix, 40% strand	Q8GME8
F	Acp-polyene thioesterase	protein	142	27% helix, 42% strand	Q8GME8
G	Acp-polyene thioesterase	protein	142	26% helix, 42% strand	Q8GME8
H	Acp-polyene thioesterase	protein	141	26% helix, 42% strand	Q8GME8

Ligands and binding sites

TAR · D(-)-tartaric acid · additive · 3 copies · chains A, B, D, C
GOL · Glycerol · additive · 2 copies · chains E, F, G, H
EDO · 1,2-ethanediol · additive · chains C, D

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

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1121	0.86	0.87	102	GOL
2	1175	0.83	0.84	99	TAR
3	137	0.78	0.95	26	empty
4	154	0.78	0.94	26	empty
5	194	0.77	0.92	30	EDO

Interfaces

14 interfaces between chains.

C–D · 1183 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 1175 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1159 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1116 Å² buried · 10 hydrogen bonds · protein-protein
E–H · 617 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

4I4J · The structure of SgcE10, the ACP-polyene thioesterase involved in C-1027 biosynthesis · 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 Q8GME8
Elsewhere: RCSB PDB 4I4J · PDBe 4I4J · UniProt Q8GME8

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