Research workbench
Crystal structure of catalytic inactive chloroplast resolvase NtMOC1 in complex with Holliday junction
Analyse Crystal structure of catalytic inactive chloroplast resolvase NtMOC1 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LCT
- Type
- protein + DNA
- Length
- 390 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Nicotiana tabacum; SYNTHETIC CONSTRUCT
- Molecule
- NtMOC1; DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*GP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3'); DNA…
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.55 · 6 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NtMOC1 | protein | 159 | 43% helix, 22% strand | — |
| B | NtMOC1 | protein | 159 | 42% helix, 21% strand | — |
| C | DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*GP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3') | dna | 18 | — | — |
| D | DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*GP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3') | dna | 18 | — | — |
| E | DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*CP*AP*AP*GP*GP*C)-3') | dna | 18 | — | — |
| F | DNA (5'-D(*AP*AP*GP*AP*TP*GP*TP*CP*CP*CP*TP*CP*TP*GP*TP*TP*GP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.73 | 0.78 | 66 | empty |
| 2 | 812 | 0.73 | 0.78 | 68 | empty |
| 3 | 56 | 0.67 | 0.96 | 24 | SO4 |
| 4 | 210 | 0.61 | 0.81 | 33 | SO4 |
| 5 | 153 | 0.47 | 0.76 | 21 | empty |
Interfaces
11 interfaces between chains.
- A–B · 914 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 668 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–F · 570 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 492 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 469 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 6LCT · Crystal structure of catalytic inactive chloroplast resolvase NTMOC1 in complex with… · 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
- Elsewhere: RCSB PDB 6LCT · PDBe 6LCT
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