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Holo-(acyl carrier protein) synthase at 1.8A

Analyse Holo-(acyl carrier protein) synthase at 1.8A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1F7T
Type: protein
Length: 713 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Holo-(acyl carrier protein) synthase
EC: 2.7.8.7
UniProt: P96618
Ligands: NA, CL
Pockets: 12 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, F	Holo-(acyl carrier protein) synthase (EC 2.7.8.7)	protein	119	40% helix, 32% strand	P96618
B, D	Holo-(acyl carrier protein) synthase (EC 2.7.8.7)	protein	119	40% helix, 29% strand	P96618
E	Holo-(acyl carrier protein) synthase (EC 2.7.8.7)	protein	118	40% helix, 30% strand	P96618

Ligands and binding sites

NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 19 copies · chains A, B, C, F, D, E
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 5 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 2 copies · chains B, C, D, F

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

Pockets

12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	224	0.55	0.78	34	GOL, CL
2	297	0.53	0.75	39	NA, CL
3	158	0.44	0.75	29	NA, CL, DTT
4	137	0.44	0.76	24	CL, DTT
5	163	0.44	0.75	27	NA, CL, DTT

Interfaces

8 interfaces between chains.

D–F · 775 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 745 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 731 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 729 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 681 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1F7T · Holo-(acyl carrier protein) synthase at 1.8A · the same entry in another collection · chain F against F, TM-score 1.00
P96618 · AlphaFold monomer V2.0 prediction for holo-[acyl-carrier-protein] synthase (P96618) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 P96618
Elsewhere: RCSB PDB 1F7T · PDBe 1F7T · UniProt P96618

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