Research workbench
Ef-tu (escherichia COLI) in complex with nvp-LDI028
Analyse Ef-tu (escherichia COLI) in complex with nvp-LDI028 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 558 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 202 Ų buried · 4 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 3U6B · PDBe 3U6B · UniProt P0CE47 · UniProt Q7M0J8
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