Research workbench
Cryo-EM structure of ecmrr-DNA complex in ecmrr-rpitc-3NT
Analyse Cryo-EM structure of ecmrr-DNA complex in ecmrr-rpitc-3NT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XLA
- Type
- protein + DNA
- Length
- 582 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Merr family transcriptional regulator ecmrr; Synthetic non-template strand DNA (54-mer)…
- Ligands
- 118
- Pockets
- 13 · best druggability 0.68
Structure
electron microscopy · 3 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H | Merr family transcriptional regulator ecmrr | protein | 268 | 41% helix, 26% strand | — |
| N | Synthetic non-template strand DNA (54-mer) | dna | 23 | — | — |
| T | Synthetic template strand DNA (54-mer) | dna | 23 | — | — |
Ligands and binding sites
- 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
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.68 | 0.78 | 68 | 118 |
| 2 | 50 | 0.68 | 0.97 | 15 | empty |
| 3 | 161 | 0.68 | 0.87 | 22 | empty |
| 4 | 432 | 0.66 | 0.78 | 44 | empty |
| 5 | 186 | 0.57 | 0.80 | 29 | empty |
Interfaces
6 interfaces between chains.
- G–H · 2614 Ų buried · 17 hydrogen bonds · protein-protein
- N–T · 1042 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- H–T · 447 Ų buried · 7 hydrogen bonds · protein-nucleic
- G–N · 374 Ų buried · 3 hydrogen bonds · protein-nucleic
- H–N · 325 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6XLA · Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPitc-3nt · the same entry in another collection · chain G against G, 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 6XLA · PDBe 6XLA
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