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Crystal structure of phosphodiesterase TW9814

Analyse Crystal structure of phosphodiesterase TW9814 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DCK
Type: protein
Length: 487 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LACTAMASE_B domain-containing protein
UniProt: A0A426W059
Ligands: MN
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LACTAMASE_B domain-containing protein	protein	246	31% helix, 27% strand	A0A426W059
B	LACTAMASE_B domain-containing protein	protein	241	31% helix, 28% strand	A0A426W059

Ligands and binding sites

MN · Manganese (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	304	0.71	0.84	52	MN

Interfaces

1 interface between chains.

A–B · 872 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7DCK · Crystal structure of phosphodiesterase tw9814 · 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 A0A426W059
Elsewhere: RCSB PDB 7DCK · PDBe 7DCK · UniProt A0A426W059

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