Research workbench
Crystal structure of escherichia COLI alkb in complex with ssdna containing a 1-methylguanine lesion
Analyse Crystal structure of escherichia COLI alkb in complex with ssdna containing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KHC
- Type
- protein + DNA
- Length
- 426 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb; DNA…
- EC
- 1.14.11.-
- UniProt
- P05050
- Ligands
- AKG, CO
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb (EC 1.14.11.-) | protein | 207 | 14% helix, 35% strand | P05050 |
| B | Alpha-ketoglutarate-dependent dioxygenase alkb (EC 1.14.11.-) | protein | 207 | 14% helix, 36% strand | P05050 |
| C | DNA (5'-D(P*TP*AP*(MG1)P*TP*GP*CP*CP*T)-3') | dna | 8 | — | — |
| D | DNA (5'-D(P*GP*CP*AP*T)-3') | dna | 4 | — | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B, C
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.61 | 0.80 | 41 | CO, AKG |
| 2 | 306 | 0.60 | 0.78 | 38 | empty |
| 3 | 90 | 0.35 | 0.75 | 15 | empty |
| 4 | 56 | 0.34 | 0.78 | 14 | empty |
| 5 | 67 | 0.27 | 0.72 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–C · 676 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 501 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 240 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- B–D · 43 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3KHC · Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a… · the same entry in another collection · chain A against A, TM-score 1.00
- P05050 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent dioxygenase alkb… · a predicted model of the same protein · chain B 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 P05050
- Elsewhere: RCSB PDB 3KHC · PDBe 3KHC · UniProt P05050
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