Research workbench
The A form apo structure of NrS-1 C terminal region-CTR
Analyse The A form apo structure of NrS-1 C terminal region-CTR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LRB
- Type
- protein
- Length
- 2,454 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.65
- Source
- Nitratiruptor phage NrS-1
- Molecule
- Primase
- UniProt
- M5AAG8
- Ligands
- MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.65 · 5 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Primase | protein | 410 | 40% helix, 19% strand | M5AAG8 |
| B | Primase | protein | 408 | 41% helix, 19% strand | M5AAG8 |
| C | Primase | protein | 410 | 40% helix, 19% strand | M5AAG8 |
| D, E | Primase | protein | 409 | 41% helix, 19% strand | M5AAG8 |
| F | Primase | protein | 408 | 41% helix, 20% strand | M5AAG8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains D, F, E
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 | 918 | 0.85 | 0.87 | 84 | MG |
| 2 | 900 | 0.85 | 0.87 | 80 | empty |
| 3 | 1010 | 0.85 | 0.85 | 90 | MG |
| 4 | 884 | 0.84 | 0.86 | 81 | empty |
| 5 | 1135 | 0.83 | 0.84 | 88 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2560 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 2539 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 2508 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 2504 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 2497 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6LRB · The a form apo structure of nrs-1 C terminal region-ctr · 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 M5AAG8
- Elsewhere: RCSB PDB 6LRB · PDBe 6LRB · UniProt M5AAG8
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