Research workbench

Response regulator pled in complex with C-digmp

Analyse Response regulator pled in complex with C-digmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1W25
Type: protein
Length: 908 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stalked-cell differentiation controlling protein
UniProt: Q9A5I5
Ligands: C2E, MG, ZN
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Stalked-cell differentiation controlling protein	protein	454	45% helix, 18% strand	Q9A5I5

Ligands and binding sites

C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 5 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
ZN · Zinc ion · metal

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	804	0.82	0.85	83	empty
2	558	0.80	0.86	54	empty
3	358	0.69	0.82	52	empty
4	156	0.48	0.77	24	empty
5	170	0.46	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 1350 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

1W25 · Response regulator PleD in complex with c-diGMP · the same entry in another collection · chain A against A, TM-score 1.00
Q9A5I5 · AlphaFold monomer V2.0 prediction for response regulator pled (Q9A5I5) · a predicted model of the same protein · chain A against A, TM-score 0.57

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 Q9A5I5
Elsewhere: RCSB PDB 1W25 · PDBe 1W25 · UniProt Q9A5I5

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