MolNFT v1 · #66702 · protein

Crystal structure of E. COLI phosphatase yrbi, with mg, tetragonal form

3HYC · 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase: “Crystal structure of E. COLI phosphatase yrbi, with mg, tetragonal form”. X-ray diffraction, 2 ligands (MG, CL), 14 pockets (best druggability 0.73). MolNFT v1 #66702 on…

PDB: 3HYC
Type: protein
Length: 1,436 residues
Chains: 8
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: MG, CL
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, F, G, H	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45)	protein	181	38% helix, 23% strand	P67653
B	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45)	protein	174	39% helix, 20% strand	P67653
D	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45)	protein	176	38% helix, 19% strand	P67653

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, H, F, G
CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E, F, G, H

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1053	0.73	0.76	123	MG, CL
2	1163	0.72	0.76	108	empty
3	328	0.62	0.79	33	MG
4	262	0.61	0.80	53	empty
5	311	0.61	0.79	58	empty

Interfaces

18 interfaces between chains.

A–B · 1181 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1178 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1169 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1169 Å² buried · 22 hydrogen bonds · protein-protein
E–H · 1109 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

3HYC · Crystal structure of E. coli phosphatase YrbI, with Mg, tetragonal form · the same entry in another collection · chain H against H, TM-score 1.00
P67653 · AlphaFold monomer V2.0 prediction for 3-deoxy-D-manno-octulosonate 8-phosphate… · 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 P67653
Elsewhere: RCSB PDB 3HYC · PDBe 3HYC · UniProt P67653

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