MolNFT v1 · #155061 · protein + DNA
Crystal structure of chloroplast resolvase in complex with holliday junction
6KVO · NTMOC1: “Crystal structure of chloroplast resolvase in complex with holliday junction”. X-ray diffraction, 2 ligands (MG, SO4), 6 pockets (best druggability 0.70). MolNFT v1 #155061 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KVO
- Type
- protein + DNA
- Length
- 396 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NTMOC1; DNA (5'- D(*AP*CP*AP*AP*CP*AP*GP*AP*TP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3'); DNA (5'…
- UniProt
- A0A1S4CVP6
- Ligands
- MG, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NTMOC1 | protein | 165 | 45% helix, 22% strand | A0A1S4CVP6 |
| B | NTMOC1 | protein | 159 | 43% helix, 21% strand | A0A1S4CVP6 |
| C | DNA (5'- D(*AP*CP*AP*AP*CP*AP*GP*AP*TP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3') | dna | 18 | — | — |
| D | DNA (5'- D(*GP*CP*CP*TP*TP*GP*CP*TP*TP*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*AP*AP*GP*CP*AP*AP*GP*GP*C)-3') | dna | 18 | — | — |
| F | DNA (5'- D(P*AP*AP*GP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*TP*TP*GP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, F, B, E
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.70 | 0.77 | 37 | empty |
| 2 | 201 | 0.69 | 0.87 | 42 | empty |
| 3 | 623 | 0.65 | 0.76 | 38 | empty |
| 4 | 214 | 0.64 | 0.83 | 32 | SO4 |
| 5 | 218 | 0.63 | 0.82 | 31 | SO4 |
Interfaces
11 interfaces between chains.
- A–B · 911 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 701 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–F · 658 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 506 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 495 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 6KVO · Crystal structure of chloroplast resolvase in complex with Holliday junction · 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 A0A1S4CVP6
- Elsewhere: RCSB PDB 6KVO · PDBe 6KVO · UniProt A0A1S4CVP6
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