Research workbench

Crystal structure of the polyketide cyclase aknh with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity.

Analyse Crystal structure of the polyketide cyclase aknh with bound substrate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F99
Type: protein
Length: 565 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aklanonic acid methyl ester cyclase, aknh
Ligands: AKV, SO4
Pockets: 7 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aklanonic acid methyl ester cyclase, aknh	protein	141	31% helix, 36% strand	—
C	Aklanonic acid methyl ester cyclase, aknh	protein	140	31% helix, 36% strand	—
D	Aklanonic acid methyl ester cyclase, aknh	protein	143	31% helix, 36% strand	—

Ligands and binding sites

AKV · {3-[(1R,3S)-1,3-dihydroxypentyl]-4,5,9,10-tetrahydroxy-2-anthryl}acetate · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	674	0.88	0.92	72	AKV
2	755	0.87	0.90	85	AKV
3	173	0.79	0.96	44	empty
4	186	0.59	0.82	32	empty
5	157	0.56	0.81	31	empty

Interfaces

6 interfaces between chains.

A–B · 1675 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 1670 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 582 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 577 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 63 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2F99 · Crystal structure of the polyketide cyclase AknH with bound substrate and product… · 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 2F99 · PDBe 2F99

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.