MolNFT v1 · #73228 · protein

1.95 ångström crystal structure of a bifunctional 3-deoxy-7- phosphoheptulonate SYNTHASE/CHORISMATE mutase (aroa) from listeria monocytogenes egd-E

3NVT · 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase: “1.95 ångström crystal structure of a bifunctional 3-deoxy-7- phosphoheptulonate SYNTHASE/CHORISMATE mutase…”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability…

PDB: 3NVT
Type: protein
Length: 672 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
EC: 2.5.1.54, 5.4.99.5
UniProt: Q8Y6T2
Ligands: MN
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (EC 2.5.1.54, 5.4.99.5)	protein	345	44% helix, 14% strand	Q8Y6T2
B	3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (EC 2.5.1.54, 5.4.99.5)	protein	327	44% helix, 15% strand	Q8Y6T2

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, B
ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	305	0.70	0.84	25	empty
2	161	0.60	0.84	26	ACT
3	176	0.58	0.82	24	ACT
4	54	0.32	0.77	15	empty
5	55	0.32	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 2377 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3NVT · 1.95 Angstrom crystal structure of a bifunctional 3-deoxy-7-phosphoheptulonate… · 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
Every structure of UniProt Q8Y6T2
Elsewhere: RCSB PDB 3NVT · PDBe 3NVT · UniProt Q8Y6T2

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