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Crystal structure of ybiv from escherichia COLI K12

Analyse Crystal structure of ybiv from escherichia COLI K12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RLM
Type: protein
Length: 1,076 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphatase
EC: 3.1.3.-
UniProt: P75792
Ligands: MG
Pockets: 9 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Phosphatase (EC 3.1.3.-)	protein	269	41% helix, 23% strand	P75792

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 6 copies · chains A, B, C, D

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	157	0.53	0.81	24	GOL
2	149	0.52	0.80	24	GOL
3	101	0.51	0.83	22	GOL
4	83	0.46	0.82	27	GOL
5	62	0.37	0.79	16	empty

Compared structures

1RLM · Crystal Structure of ybiV from Escherichia coli K12 · the same entry in another collection · chain A against A, TM-score 1.00
P75792 · AlphaFold monomer V2.0 prediction for sugar phosphatase ybiv (P75792) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P75792
Elsewhere: RCSB PDB 1RLM · PDBe 1RLM · UniProt P75792

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