MolNFT v1 · #169722 · protein + DNA
Cryo-EM structure of ecmrr-DNA complex in ecmrr-rpo
6XL6 · Synthetic non-template strand DNA (54-mer): “Cryo-EM structure of ecmrr-DNA complex in ecmrr-rpo”. Electron microscopy, 2 ligands (1N7, 118), 14 pockets (best druggability 0.69). MolNFT v1 #169722 on GenesisL1: 3D structure, binding…
- PDB
- 6XL6
- Type
- protein + DNA
- Length
- 582 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synthetic non-template strand DNA (54-mer); Synthetic template strand DNA (54-mer); Merr…
- Ligands
- 1N7, 118
- Pockets
- 14 · best druggability 0.69
Structure
electron microscopy · 3 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Synthetic non-template strand DNA (54-mer) | dna | 23 | — | — |
| T | Synthetic template strand DNA (54-mer) | dna | 23 | — | — |
| G, H | Merr family transcriptional regulator ecmrr | protein | 268 | 39% helix, 26% strand | — |
Ligands and binding sites
- 1N7 · Chapso · ligand · 2 copies · chains G, H
- 118 · Tetraphenylantimonium ion · ligand · 2 copies · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.69 | 0.82 | 26 | 1N7 |
| 2 | 350 | 0.65 | 0.79 | 27 | 1N7 |
| 3 | 394 | 0.64 | 0.78 | 49 | 118 |
| 4 | 319 | 0.60 | 0.78 | 50 | 118 |
| 5 | 212 | 0.52 | 0.77 | 21 | empty |
Interfaces
6 interfaces between chains.
- G–H · 2845 Ų buried · 25 hydrogen bonds · protein-protein
- N–T · 1015 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- T–H · 469 Ų buried · 13 hydrogen bonds · protein-nucleic
- N–G · 409 Ų buried · 9 hydrogen bonds · protein-nucleic
- N–H · 345 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6XL6 · Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPo · the same entry in another collection · chain N against N, 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
- Elsewhere: RCSB PDB 6XL6 · PDBe 6XL6
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