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The apo structure of methanococcus jannaschii phosphodiesterase MJ0936

Analyse The apo structure of methanococcus jannaschii phosphodiesterase MJ0936 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2AHD
Type: protein
Length: 660 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphodiesterase MJ0936
EC: 3.1.4.-
UniProt: Q58346
Pockets: 3 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Phosphodiesterase MJ0936 (EC 3.1.4.-)	protein	165	24% helix, 32% strand	Q58346

Pockets

3 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	184	0.50	0.77	28	empty
2	93	0.37	0.75	19	empty
3	80	0.33	0.74	19	empty

Interfaces

3 interfaces between chains.

A–D · 648 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 542 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 541 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2AHD · The Apo structure of Methanococcus jannaschii phosphodiesterase MJ0936 · the same entry in another collection · chain A against A, TM-score 1.00
Q58346 · AlphaFold monomer V2.0 prediction for phosphodiesterase MJ0936 (Q58346) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q58346
Elsewhere: RCSB PDB 2AHD · PDBe 2AHD · UniProt Q58346

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