MolNFT v1 · #83278 · protein

Typeiii polyketide synthases

3WD8 · Type III polyketide synthase quinolone synthase: “Typeiii polyketide synthases”. X-ray diffraction, 15 pockets (best druggability 0.72). MolNFT v1 #83278 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WD8
Type: protein
Length: 1,564 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type III polyketide synthase quinolone synthase
Pockets: 15 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Type III polyketide synthase quinolone synthase	protein	391	42% helix, 24% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	298	0.72	0.85	45	empty
2	317	0.72	0.84	41	empty
3	279	0.71	0.85	37	GOL
4	258	0.69	0.84	32	empty
5	50	0.60	0.93	16	empty

Interfaces

3 interfaces between chains.

C–D · 3323 Å² buried · 59 hydrogen bonds · protein-protein
A–B · 3307 Å² buried · 57 hydrogen bonds · protein-protein
B–C · 208 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3WD8 · TypeIII polyketide synthases · 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 3WD8 · PDBe 3WD8

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