MolNFT v1 · #80755 · protein

Ef-tu (escherichia COLI) in complex with nvp-LDK733

3U6K · Elongation factor tu 1: “Ef-tu (escherichia COLI) in complex with nvp-LDK733”. X-ray diffraction, 3 ligands (9BB, GDP, MG), 9 pockets (best druggability 0.59). MolNFT v1 #80755 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3U6K
Type: protein
Length: 794 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongation factor tu 1; Thiocillin GE2270 analogue nvp-LDK733
UniProt: P0CE47, Q7M0J8
Ligands: 9BB, GDP, MG
Pockets: 9 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Elongation factor tu 1	protein	386	24% helix, 38% strand	P0CE47
C, D	Thiocillin GE2270 analogue nvp-LDK733	protein	11	0% helix, 0% strand	Q7M0J8

Ligands and binding sites

9BB · Trans-4-({[(E)-1-amino-2-sulfanylethenyl]carbamoyl}oxy)cyclohexanecarboxylic acid · ligand · 2 copies · chains A, C, B, D
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

9 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	337	0.59	0.76	44	empty
2	144	0.41	0.74	26	empty
3	105	0.40	0.76	20	empty
4	118	0.40	0.75	19	empty
5	60	0.34	0.77	15	empty

Interfaces

3 interfaces between chains.

B–D · 564 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 563 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 466 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

3U6K · Ef-tu (escherichia coli) in complex with nvp-ldk733 · the same entry in another collection · chain A against A, TM-score 1.00
P0CE47 · AlphaFold monomer V2.0 prediction for elongation factor tu 1 (P0CE47) · a predicted model of the same protein · chain A against A, TM-score 0.59

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 P0CE47
Every structure of UniProt Q7M0J8
Elsewhere: RCSB PDB 3U6K · PDBe 3U6K · UniProt P0CE47 · UniProt Q7M0J8

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