MolNFT v1 · #137337 · protein
Crystal structure of eilr in complex with malachite green
5VLG · Regulatory protein tetr: “Crystal structure of eilr in complex with malachite green”. X-ray diffraction, 1 ligand (MGR), 15 pockets (best druggability 0.79). MolNFT v1 #137337 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5VLG
- Type
- protein
- Length
- 1,510 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein tetr
- UniProt
- E3G817
- Ligands
- MGR
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Regulatory protein tetr | protein | 188 | 77% helix, 0% strand | E3G817 |
| B, D, H | Regulatory protein tetr | protein | 189 | 77% helix, 0% strand | E3G817 |
| F | Regulatory protein tetr | protein | 191 | 74% helix, 0% strand | E3G817 |
Ligands and binding sites
- MGR · Malachite green · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.79 | 0.85 | 54 | MGR |
| 2 | 514 | 0.79 | 0.85 | 52 | MGR |
| 3 | 240 | 0.78 | 0.91 | 35 | MGR |
| 4 | 816 | 0.77 | 0.81 | 92 | MGR |
| 5 | 232 | 0.74 | 0.88 | 27 | MGR |
Interfaces
8 interfaces between chains.
- E–F · 1452 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1436 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 1435 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1427 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1153 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5VLG · Crystal structure of EilR in complex with malachite green · 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 E3G817
- Elsewhere: RCSB PDB 5VLG · PDBe 5VLG · UniProt E3G817
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