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Crystal structure of the tatd deoxyribonuclease MW0446 from staphylococcus aureus. northeast structural genomics consortium target ZR237.

Analyse Crystal structure of the tatd deoxyribonuclease MW0446 from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GZX
Type: protein
Length: 506 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative tatd related DNase
UniProt: Q1Y6Z0
Ligands: NI
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative tatd related DNase	protein	253	49% helix, 17% strand	Q1Y6Z0

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.72	0.76	82	NI

Interfaces

1 interface between chains.

A–B · 598 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

2GZX · Crystal Structure of the TatD deoxyribonuclease MW0446 from Staphylococcus aureus.… · 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 Q1Y6Z0
Elsewhere: RCSB PDB 2GZX · PDBe 2GZX · UniProt Q1Y6Z0

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