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Crystal structure of ycfh, tatd homolog from escherichia COLI K12, at 1.9 a resolution

Analyse Crystal structure of ycfh, tatd homolog from escherichia COLI K12, at 1.9 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YIX
Type: protein
Length: 530 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyribonuclease ycfh
EC: 3.1.21.-
UniProt: P37346
Ligands: ZN
Pockets: 2 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Deoxyribonuclease ycfh (EC 3.1.21.-)	protein	265	46% helix, 17% strand	P37346

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	180	0.46	0.75	25	ZN
2	139	0.42	0.75	27	empty

Interfaces

1 interface between chains.

A–B · 188 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1YIX · Crystal structure of YCFH, TATD homolog from Escherichia coli K12, at 1.9 A resolution · the same entry in another collection · chain B against B, 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 P37346
Elsewhere: RCSB PDB 1YIX · PDBe 1YIX · UniProt P37346

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