MolNFT v1 · #38488 · protein

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

2GZX · Putative tatd related DNase: “Crystal structure of the tatd deoxyribonuclease MW0446 from staphylococcus aureus. northeast structural…”. X-ray diffraction, 1 ligand (NI), 1 pocket (best druggability 0.72). MolNFT v1 #38488 on…

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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