Research workbench
Crystal structure of the mitochondrial DNA packaging protein ABF2P in complex with DNA at 2.6 ångström resolution
Analyse Crystal structure of the mitochondrial DNA packaging protein ABF2P in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JGH
- Type
- protein + DNA
- Length
- 794 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ars-binding factor 2, mitochondrial; DNA (5'- D(*TP*TP*TP*AP*TP*TP*AP*TP*TP*TP*TP*AP*TP*AP…
- UniProt
- Q02486
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Ars-binding factor 2, mitochondrial | protein | 156 | 76% helix, 0% strand | Q02486 |
| B, E, H, K | DNA (5'- D(*TP*TP*TP*AP*TP*TP*AP*TP*TP*TP*TP*AP*TP*AP*TP*TP*AP*TP*AP*TP*AP*A)- 3') | dna | 22 | — | — |
| C, F, I, L | DNA (5'- D(*TP*TP*AP*TP*AP*TP*AP*AP*TP*AP*TP*AP*AP*AP*AP*TP*AP*AP*TP*AP*AP*A)- 3') | dna | 22 | — | — |
| D | Ars-binding factor 2, mitochondrial | protein | 155 | 77% helix, 0% strand | Q02486 |
| J | Ars-binding factor 2, mitochondrial | protein | 151 | 75% helix, 0% strand | Q02486 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.65 | 0.75 | 44 | empty |
| 2 | 108 | 0.63 | 0.89 | 24 | empty |
| 3 | 567 | 0.62 | 0.75 | 35 | empty |
| 4 | 406 | 0.57 | 0.75 | 33 | empty |
| 5 | 393 | 0.56 | 0.74 | 32 | empty |
Interfaces
36 interfaces between chains.
- E–F · 1000 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- H–I · 996 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- K–L · 991 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- B–C · 981 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- A–B · 748 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 5JGH · Crystal structure of the mitochondrial DNA packaging protein Abf2p in complex with DNA at… · the same entry in another collection · chain L against L, 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 Q02486
- Elsewhere: RCSB PDB 5JGH · PDBe 5JGH · UniProt Q02486
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