Research workbench
Ef-tu (escherichia COLI) in complex with nvp-LDK733
Analyse Ef-tu (escherichia COLI) in complex with nvp-LDK733 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 563 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 466 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
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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