MolNFT v1 · #83589 · protein

Crystal structure of ef-pyl in complex with gmppnp

3WNB · Protein translation elongation factor 1A: “Crystal structure of ef-pyl in complex with gmppnp”. X-ray diffraction, 2 ligands (GNP, MG), 4 pockets (best druggability 0.68). MolNFT v1 #83589 on GenesisL1: 3D structure, binding sites…

PDB: 3WNB
Type: protein
Length: 361 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein translation elongation factor 1A
UniProt: Q8PXB3
Ligands: GNP, MG
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein translation elongation factor 1A	protein	361	20% helix, 43% strand	Q8PXB3

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
MG · Magnesium ion · metal · 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	371	0.68	0.81	29	empty
2	137	0.50	0.79	21	empty
3	78	0.39	0.78	22	empty
4	66	0.32	0.75	13	empty

Modifications

Observed in the structure: 5 modified (engineered).

Compared structures

3WNB · Crystal structure of EF-Pyl in complex with GMPPNP · 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 Q8PXB3
Elsewhere: RCSB PDB 3WNB · PDBe 3WNB · UniProt Q8PXB3

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