MolNFT v1 · #90760 · protein + DNA
A new twist on the translocation mechanism of helicases from the structure of dnab with its substrates
4ESV · 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3': “A new twist on the translocation mechanism of helicases from the structure of dnab with its substrates”. X-ray diffraction, 3 ligands (GDP, ALF, CA), 20 pockets (best…
- PDB
- 4ESV
- Type
- protein + DNA
- Length
- 5,099 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'…
- EC
- 3.6.4.12
- UniProt
- Q9X4C9
- Ligands
- GDP, ALF, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 14 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | dna | 14 | — | — |
| W | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | dna | 13 | — | — |
| A | Replicative helicase (EC 3.6.4.12) | protein | 418 | 50% helix, 13% strand | Q9X4C9 |
| B | Replicative helicase (EC 3.6.4.12) | protein | 430 | 49% helix, 11% strand | Q9X4C9 |
| C | Replicative helicase (EC 3.6.4.12) | protein | 434 | 53% helix, 12% strand | Q9X4C9 |
| D | Replicative helicase (EC 3.6.4.12) | protein | 431 | 53% helix, 13% strand | Q9X4C9 |
| E | Replicative helicase (EC 3.6.4.12) | protein | 418 | 54% helix, 13% strand | Q9X4C9 |
| F | Replicative helicase (EC 3.6.4.12) | protein | 421 | 53% helix, 13% strand | Q9X4C9 |
| G | Replicative helicase (EC 3.6.4.12) | protein | 421 | 51% helix, 12% strand | Q9X4C9 |
| H | Replicative helicase (EC 3.6.4.12) | protein | 425 | 50% helix, 12% strand | Q9X4C9 |
| I | Replicative helicase (EC 3.6.4.12) | protein | 418 | 51% helix, 12% strand | Q9X4C9 |
| J | Replicative helicase (EC 3.6.4.12) | protein | 416 | 51% helix, 13% strand | Q9X4C9 |
| K | Replicative helicase (EC 3.6.4.12) | protein | 421 | 51% helix, 12% strand | Q9X4C9 |
| L | Replicative helicase (EC 3.6.4.12) | protein | 419 | 52% helix, 12% strand | Q9X4C9 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 10 copies · chains A, F, B, C, D, E, G, L, H, I, J, K
- ALF · Tetrafluoroaluminate ion · ligand · 10 copies · chains A, F, B, C, D, E, G, L, H, I, J, K
- CA · Calcium ion · metal · 14 copies · chains A, V, F, B, C, D, E, G, I, L
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains W, H, I, C, E, F, J
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 | 915 | 0.79 | 0.82 | 106 | ALF, GDP, CA |
| 2 | 690 | 0.78 | 0.83 | 79 | GDP, CA, ALF |
| 3 | 772 | 0.78 | 0.82 | 70 | GDP, CA, ALF |
| 4 | 1014 | 0.78 | 0.80 | 87 | CA |
| 5 | 937 | 0.76 | 0.79 | 105 | CA |
Interfaces
30 interfaces between chains.
- C–D · 3411 Ų buried · 27 hydrogen bonds · protein-protein
- K–L · 3247 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 3169 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 3068 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2963 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4ESV · A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with… · the same entry in another collection · chain C against C, 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 Q9X4C9
- Elsewhere: RCSB PDB 4ESV · PDBe 4ESV · UniProt Q9X4C9
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