MolNFT v1 · #50119 · protein

Crystal structure of yrbi phosphatase from escherichia COLI

2R8X · 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase: “Crystal structure of yrbi phosphatase from escherichia COLI”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.79). MolNFT v1 #50119 on GenesisL1: 3D structure…

PDB: 2R8X
Type: protein
Length: 2,889 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
EC: 3.1.3.45
UniProt: P67653
Ligands: CL
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, G, I, J, K, L, M, N, O, P	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45)	protein	181	36% helix, 19% strand	P67653
F	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45)	protein	172	40% helix, 20% strand	P67653
H	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45)	protein	183	36% helix, 21% strand	P67653

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, B, C, D, G, H

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	884	0.79	0.82	76	empty
2	535	0.68	0.78	64	empty
3	315	0.65	0.81	34	empty
4	591	0.65	0.75	57	empty
5	557	0.63	0.75	53	empty

Interfaces

37 interfaces between chains.

M–N · 1198 Å² buried · 24 hydrogen bonds · protein-protein
F–G · 1192 Å² buried · 22 hydrogen bonds · protein-protein
J–K · 1187 Å² buried · 22 hydrogen bonds · protein-protein
E–H · 1183 Å² buried · 21 hydrogen bonds · protein-protein
I–J · 1182 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

2R8X · Crystal structure of YrbI phosphatase from Escherichia coli · the same entry in another collection · chain P against P, 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 P67653
Elsewhere: RCSB PDB 2R8X · PDBe 2R8X · UniProt P67653

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.