MolNFT v1 · #185389 · protein

Actinobacterial 2-hydroxyacyl-CoA lyase (achacl) mutant E493A structure in complex with substrate 2-hib-CoA and inactive cofactor 3-deaza-thdp

7PT3: “Actinobacterial 2-hydroxyacyl-CoA lyase (achacl) mutant E493A structure in complex with substrate 2-hib-CoA…”. X-ray diffraction, 3 ligands (TPW, 3KK, MG), 7 pockets (best druggability 0.85). MolNFT v1 #185389 on GenesisL1: 3D…

PDB: 7PT3
Type: protein
Length: 1,146 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-hydroxyacyl-CoA lyase
EC: 4.2.1.17
Ligands: TPW, 3KK, MG
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-hydroxyacyl-CoA lyase (EC 4.2.1.17)	protein	574	45% helix, 17% strand	—
B	2-hydroxyacyl-CoA lyase (EC 4.2.1.17)	protein	572	45% helix, 17% strand	—

Ligands and binding sites

TPW · 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
3KK · S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3, 5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2, 4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxy-2-methylpropanethioate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 3 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	871	0.85	0.87	89	TPW, 3KK, MG
2	904	0.85	0.86	92	TPW, 3KK
3	128	0.78	0.97	39	MG
4	365	0.70	0.83	50	empty
5	383	0.69	0.82	56	empty

Interfaces

1 interface between chains.

A–B · 3434 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

7PT3 · Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493A structure in complex with… · 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 7PT3 · PDBe 7PT3

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