MolNFT v1 · #34304 · protein

Crystal structure of the GTP-binding protein ychf in complexed with GDP

2DBY: “Crystal structure of the GTP-binding protein ychf in complexed with GDP”. X-ray diffraction, 1 ligand (GDP), 4 pockets (best druggability 0.60). MolNFT v1 #34304 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2DBY
Type: protein
Length: 355 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding protein
UniProt: Q5SJ29
Ligands: GDP
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding protein	protein	355	48% helix, 19% strand	Q5SJ29

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
FMT · Formic acid · additive · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	221	0.60	0.81	32	empty
2	171	0.49	0.77	21	empty
3	130	0.37	0.73	22	empty
4	52	0.29	0.75	14	empty

Modifications

Observed in the structure: 2 modified (engineered).

Compared structures

2DBY · Crystal structure of the GTP-binding protein YchF in complexed with GDP · 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 Q5SJ29
Elsewhere: RCSB PDB 2DBY · PDBe 2DBY · UniProt Q5SJ29

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