MolNFT v1 · #51730 · protein

RV2361 native

2VG4 · Undecaprenyl pyrophosphate synthetase: “RV2361 native”. X-ray diffraction, 9 pockets (best druggability 0.82). MolNFT v1 #51730 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VG4
Type: protein
Length: 1,135 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Undecaprenyl pyrophosphate synthetase
EC: 2.5.1.31
UniProt: P60479
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31)	protein	284	37% helix, 13% strand	P60479
D	Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31)	protein	283	36% helix, 14% strand	P60479

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	210	0.82	0.96	37	empty
2	441	0.81	0.88	58	empty
3	169	0.79	0.95	35	empty
4	1168	0.79	0.81	123	empty
5	65	0.41	0.80	14	empty

Interfaces

4 interfaces between chains.

B–D · 2235 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 2217 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 686 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 480 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2VG4 · Rv2361 native · 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 P60479
Elsewhere: RCSB PDB 2VG4 · PDBe 2VG4 · UniProt P60479

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