MolNFT v1 · #153842 · protein + DNA
Crystal structure of ZMMOC1-holliday junction complex in the presence of calcium
6JRF · Monokaryotic chloroplast 1: “Crystal structure of ZMMOC1-holliday junction complex in the presence of calcium”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.73). MolNFT v1 #153842 on GenesisL1: 3D structure…
- PDB
- 6JRF
- Type
- protein + DNA
- Length
- 387 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monokaryotic chloroplast 1; DNA (33-mer)
- UniProt
- B4FCI7
- Ligands
- CA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Monokaryotic chloroplast 1 | protein | 163 | 44% helix, 23% strand | B4FCI7 |
| C | DNA (33-mer) | dna | 30 | — | — |
| D | DNA (33-mer) | dna | 31 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, D, B, C
- 1PE · Pentaethylene glycol · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.73 | 0.77 | 71 | 1PE |
| 2 | 760 | 0.69 | 0.76 | 41 | empty |
| 3 | 51 | 0.68 | 0.97 | 22 | empty |
| 4 | 216 | 0.57 | 0.79 | 32 | empty |
| 5 | 60 | 0.28 | 0.74 | 11 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1085 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 1080 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 898 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 840 Ų buried · 95 hydrogen bonds · nucleic-nucleic
- B–D · 619 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 6JRF · Crystal structure of ZmMoc1-Holliday junction Complex in the presence of Calcium · 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 B4FCI7
- Elsewhere: RCSB PDB 6JRF · PDBe 6JRF · UniProt B4FCI7
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