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Crystal structure of metallophosphoesterase from sphaerobacter thermophilus

Analyse Crystal structure of metallophosphoesterase from sphaerobacter thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RQZ
Type: protein
Length: 727 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallophosphoesterase
UniProt: D1C4A9
Ligands: ZN
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metallophosphoesterase	protein	243	36% helix, 20% strand	D1C4A9
B	Metallophosphoesterase	protein	239	35% helix, 19% strand	D1C4A9
C	Metallophosphoesterase	protein	245	33% helix, 20% strand	D1C4A9

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C
ACT · Acetate ion · additive · chains C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	384	0.69	0.81	49	empty
2	361	0.68	0.81	47	empty
3	56	0.41	0.82	16	empty
4	87	0.39	0.77	20	empty
5	128	0.39	0.74	27	empty

Interfaces

2 interfaces between chains.

B–C · 1247 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1132 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

3RQZ · Crystal structure of metallophosphoesterase from Sphaerobacter thermophilus · 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 D1C4A9
Elsewhere: RCSB PDB 3RQZ · PDBe 3RQZ · UniProt D1C4A9

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