MolNFT v1 · #152756 · protein + DNA
Crystal structure of ZMMOC1 D115N mutant in complex with holliday junction
6IS8 · Monokaryotic chloroplast 1: “Crystal structure of ZMMOC1 D115N mutant in complex with holliday junction”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.72). MolNFT v1 #152756 on GenesisL1: 3D structure, binding…
- PDB
- 6IS8
- Type
- protein + DNA
- Length
- 391 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
- MG
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Monokaryotic chloroplast 1 | protein | 163 | 45% helix, 23% strand | B4FCI7 |
| C | DNA (33-mer) | dna | 33 | — | — |
| D | DNA (33-mer) | dna | 32 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.72 | 0.98 | 21 | empty |
| 2 | 669 | 0.69 | 0.77 | 44 | empty |
| 3 | 677 | 0.68 | 0.76 | 39 | empty |
| 4 | 246 | 0.60 | 0.79 | 27 | 1PE |
| 5 | 217 | 0.59 | 0.80 | 29 | 1PE |
Interfaces
6 interfaces between chains.
- A–D · 1105 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 1092 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 926 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 830 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- B–D · 588 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 6IS8 · Crystal structure of ZmMoc1 D115N mutant 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 B4FCI7
- Elsewhere: RCSB PDB 6IS8 · PDBe 6IS8 · UniProt B4FCI7
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