Research workbench

Pentaketide chromone synthase complexed with coenzyme a

Analyse Pentaketide chromone synthase complexed with coenzyme a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2D3M
Type: protein
Length: 800 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pentaketide chromone synthase
Ligands: COA
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pentaketide chromone synthase	protein	405	40% helix, 23% strand	—
B	Pentaketide chromone synthase	protein	395	43% helix, 24% strand	—

Ligands and binding sites

COA · Coenzyme A · ligand · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	227	0.63	0.82	30	COA
2	228	0.63	0.82	30	COA
3	256	0.61	0.80	29	empty
4	142	0.50	0.79	23	empty
5	60	0.41	0.81	16	empty

Interfaces

1 interface between chains.

A–B · 3480 Å² buried · 85 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

2D3M · Pentaketide chromone synthase complexed with coenzyme A · 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
Elsewhere: RCSB PDB 2D3M · PDBe 2D3M

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