Research workbench
Crystal structure of the overoxidized abfr bound to DNA
Analyse Crystal structure of the overoxidized abfr bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HLH
- Type
- protein + DNA
- Length
- 1,276 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP* GP*T)-3')…
- UniProt
- A0A0N1EJ89
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 69% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J, K, L, M, N, O, P | DNA (5'- D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP* GP*T)-3') | dna | 24 | — | — |
| A | Marr family transcriptional regulator | protein | 135 | 70% helix, 9% strand | A0A0N1EJ89 |
| B | Marr family transcriptional regulator | protein | 138 | 71% helix, 9% strand | A0A0N1EJ89 |
| C | Marr family transcriptional regulator | protein | 133 | 68% helix, 9% strand | A0A0N1EJ89 |
| D | Marr family transcriptional regulator | protein | 136 | 71% helix, 9% strand | A0A0N1EJ89 |
| E | Marr family transcriptional regulator | protein | 137 | 69% helix, 9% strand | A0A0N1EJ89 |
| F, H | Marr family transcriptional regulator | protein | 137 | 69% helix, 9% strand | A0A0N1EJ89 |
| G | Marr family transcriptional regulator | protein | 131 | 66% helix, 9% strand | A0A0N1EJ89 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.79 | 0.84 | 51 | empty |
| 2 | 740 | 0.77 | 0.82 | 55 | empty |
| 3 | 718 | 0.77 | 0.82 | 57 | empty |
| 4 | 728 | 0.76 | 0.81 | 52 | empty |
| 5 | 462 | 0.62 | 0.76 | 43 | empty |
Interfaces
33 interfaces between chains.
- E–F · 2829 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2825 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2796 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2743 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 1001 Ų buried · 82 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 5HLH · Crystal structure of the overoxidized AbfR bound to DNA · the same entry in another collection · chain I against I, 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 A0A0N1EJ89
- Elsewhere: RCSB PDB 5HLH · PDBe 5HLH · UniProt A0A0N1EJ89
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