MolNFT v1 · #74714 · protein

Helicase domain of reverse gyrase from thermotoga maritima

3P4X · Reverse gyrase helicase-like domain: “Helicase domain of reverse gyrase from thermotoga maritima”. X-ray diffraction, 3 ligands (ADP, MG, CL), 9 pockets (best druggability 0.87). MolNFT v1 #74714 on GenesisL1: 3D structure, binding…

PDB: 3P4X
Type: protein
Length: 809 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reverse gyrase helicase-like domain
Ligands: ADP, MG, CL
Pockets: 9 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Reverse gyrase helicase-like domain	protein	399	46% helix, 17% strand	—
B	Reverse gyrase helicase-like domain	protein	410	49% helix, 15% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
CL · Chloride ion · ion · chains B

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

Pockets

9 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	1156	0.87	0.88	113	empty
2	1145	0.83	0.84	91	empty
3	52	0.51	0.87	17	empty
4	93	0.46	0.80	15	empty
5	95	0.39	0.77	24	empty

Interfaces

1 interface between chains.

A–B · 2328 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

3P4X · Helicase domain of reverse gyrase from Thermotoga maritima · 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 3P4X · PDBe 3P4X

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