MolNFT v1 · #89712 · protein

2.52 ångström resolution crystal structure of the acyl-carrier-protein synthase (acps)-acyl carrier protein (acp) protein-protein complex from staphylococcus aureus subsp. aureus col

4DXE: “2.52 ångström resolution crystal structure of the acyl-carrier-protein synthase (acps)-acyl carrier protein…”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #89712 on GenesisL1: 3D structure, binding sites and…

PDB: 4DXE
Type: protein
Length: 1,130 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-carrier-protein synthase; Acyl carrier protein
EC: 2.7.8.7
UniProt: Q5HED0, Q5HGK0
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 9 distinct chains · 51% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Acyl-carrier-protein synthase (EC 2.7.8.7)	protein	113	43% helix, 30% strand	Q5HED0
B	Acyl-carrier-protein synthase (EC 2.7.8.7)	protein	111	44% helix, 29% strand	Q5HED0
C	Acyl-carrier-protein synthase (EC 2.7.8.7)	protein	112	44% helix, 31% strand	Q5HED0
E	Acyl-carrier-protein synthase (EC 2.7.8.7)	protein	113	43% helix, 33% strand	Q5HED0
F	Acyl-carrier-protein synthase (EC 2.7.8.7)	protein	113	43% helix, 31% strand	Q5HED0
H	Acyl carrier protein	protein	74	55% helix, 3% strand	Q5HGK0
L, J	Acyl carrier protein	protein	76	64% helix, 3% strand	Q5HGK0
K, G	Acyl carrier protein	protein	76	66% helix, 3% strand	Q5HGK0
I	Acyl carrier protein	protein	77	68% helix, 3% strand	Q5HGK0

Ligands and binding sites

MLI · Malonate ion · additive · 4 copies · chains A, B, C, I, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	408	0.80	0.88	70	empty
2	257	0.74	0.88	48	empty
3	203	0.73	0.89	40	empty
4	177	0.72	0.90	36	empty
5	173	0.70	0.89	30	empty

Interfaces

33 interfaces between chains.

E–F · 847 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 834 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 820 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 818 Å² buried · 10 hydrogen bonds · protein-protein
F–L · 789 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

4DXE · 2.52 Angstrom resolution crystal structure of the acyl-carrier-protein synthase… · the same entry in another collection · chain I against I, 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
Every structure of UniProt Q5HED0
Every structure of UniProt Q5HGK0
Elsewhere: RCSB PDB 4DXE · PDBe 4DXE · UniProt Q5HED0 · UniProt Q5HGK0

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