MolNFT v1 · #80746 · protein

Ef-tu (escherichia COLI) in complex with nvp-LDI028

3U6B · Elongation factor tu 1: “Ef-tu (escherichia COLI) in complex with nvp-LDI028”. X-ray diffraction, 3 ligands (8BB, GDP, MG), 3 pockets (best druggability 0.61). MolNFT v1 #80746 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3U6B
Type: protein
Length: 767 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongation factor tu 1; Thiocillin GE2270 analogue nvp-LDI028
UniProt: P0CE47, Q7M0J8
Ligands: 8BB, GDP, MG
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Elongation factor tu 1	protein	369	24% helix, 37% strand	P0CE47
B	Elongation factor tu 1	protein	376	25% helix, 36% strand	P0CE47
C, D	Thiocillin GE2270 analogue nvp-LDI028	protein	11	0% helix, 0% strand	Q7M0J8

Ligands and binding sites

8BB · Trans-4-{[(E)-1-amino-2-sulfanylethenyl]carbamoyl}cyclohexanecarboxylic acid · ligand · 2 copies · chains B, C, A, 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

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	492	0.61	0.75	64	empty
2	334	0.54	0.75	46	empty
3	192	0.42	0.72	41	empty

Interfaces

3 interfaces between chains.

B–C · 569 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 558 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 202 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3U6B · Ef-tu (escherichia coli) in complex with nvp-ldi028 · 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 0.60

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 3U6B · PDBe 3U6B · UniProt P0CE47 · UniProt Q7M0J8

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