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Structural studies of streptococcus pneumoniae epsp synthase, tetrahedral intermediate bound state

Analyse Structural studies of streptococcus pneumoniae epsp synthase, tetrahedral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RF4
Type: protein
Length: 1,708 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5-enolpyruvylshikimate-3-phosphate synthase
EC: 2.5.1.19
UniProt: Q9S400
Ligands: SPQ
Pockets: 12 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19)	protein	427	34% helix, 27% strand	Q9S400

Ligands and binding sites

SPQ · (3R,4S,5R)-5-{[(1R)-1-carboxy-2-fluoro-1-(phosphonooxy)ethyl]oxy}-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

12 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	1001	0.80	0.81	90	empty
2	113	0.76	0.96	30	SPQ
3	555	0.74	0.81	53	empty
4	170	0.73	0.91	36	SPQ
5	162	0.72	0.91	37	SPQ

Interfaces

4 interfaces between chains.

A–B · 411 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 384 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 303 Å² buried · 1 hydrogen bond · protein-protein
A–C · 273 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1RF4 · Structural Studies of Streptococcus pneumoniae EPSP Synthase, Tetrahedral intermediate… · the same entry in another collection · chain D against D, TM-score 1.00
Q9S400 · AlphaFold monomer V2.0 prediction for 3-phosphoshikimate 1-carboxyvinyltransferase… · a predicted model of the same protein · chain D 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
Every structure of UniProt Q9S400
Elsewhere: RCSB PDB 1RF4 · PDBe 1RF4 · UniProt Q9S400

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