Research workbench
Cryo-EM structure of the mukbef-matp-DNA head module
Analyse Cryo-EM structure of the mukbef-matp-DNA head module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NYW
- Type
- protein + DNA
- Length
- 2,899 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromosome partition protein mukb; Chromosome partition protein mukf; Chromosome…
- UniProt
- A0A0F7LRY2, A0A0F7LMQ4, A0A0F7LPV6, A0A6D2XA84, A0A0F7LUV5
- Ligands
- ATP, PNS, MG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 12 distinct chains · 60% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromosome partition protein mukb | protein | 685 | 54% helix, 17% strand | A0A0F7LRY2 |
| B | Chromosome partition protein mukb | protein | 858 | 61% helix, 13% strand | A0A0F7LRY2 |
| C | Chromosome partition protein mukf | protein | 335 | 69% helix, 8% strand | A0A0F7LMQ4 |
| D | Chromosome partition protein mukf | protein | 94 | 59% helix, 11% strand | A0A0F7LMQ4 |
| E | Chromosome partition protein muke | protein | 212 | 54% helix, 13% strand | A0A0F7LPV6 |
| F | Chromosome partition protein muke | protein | 198 | 54% helix, 12% strand | A0A0F7LPV6 |
| G, H | Acyl carrier protein | protein | 72 | 53% helix, 3% strand | A0A6D2XA84 |
| I | Macrodomain ter protein | protein | 134 | 70% helix, 7% strand | A0A0F7LUV5 |
| J | Macrodomain ter protein | protein | 135 | 74% helix, 7% strand | A0A0F7LUV5 |
| K | MATS2 DNA 80 B, oligo FBA769 | dna | 22 | — | — |
| L | MATS2 DNA 80 B, oligo FBA770 | dna | 22 | — | — |
| M, N | DNA 80 B | dna | 30 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- PNS · 4'-phosphopantetheine · ligand · 2 copies · chains A, B, G, H
- 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
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.78 | 0.82 | 81 | empty |
| 2 | 490 | 0.78 | 0.86 | 59 | empty |
| 3 | 500 | 0.78 | 0.85 | 54 | empty |
| 4 | 896 | 0.77 | 0.80 | 70 | empty |
| 5 | 123 | 0.76 | 0.95 | 21 | empty |
Interfaces
34 interfaces between chains.
- A–B · 2707 Ų buried · 45 hydrogen bonds · protein-protein
- C–E · 2111 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 1725 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1557 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1477 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (phosphopantetheinylation).
Compared structures
- 7NYW · Cryo-EM structure of the MukBEF-MatP-DNA head module · 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 A0A0F7LRY2
- Every structure of UniProt A0A0F7LMQ4
- Every structure of UniProt A0A0F7LPV6
- Every structure of UniProt A0A6D2XA84
- Every structure of UniProt A0A0F7LUV5
- Elsewhere: RCSB PDB 7NYW · PDBe 7NYW · UniProt A0A0F7LRY2 · UniProt A0A0F7LMQ4 · UniProt A0A0F7LPV6 · UniProt A0A6D2XA84 · UniProt A0A0F7LUV5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.