MolNFT v1 · #99771 · protein + DNA
Structure of bacterial polynucleotide kinase michaelis complex bound to GTP and DNA
4MDF · Metallophosphoesterase: “Structure of bacterial polynucleotide kinase michaelis complex bound to GTP and DNA”. X-ray diffraction, 2 ligands (GTP, MG), 5 pockets (best druggability 0.62). MolNFT v1 #99771 on GenesisL1: 3D structure…
- PDB
- 4MDF
- Type
- protein + DNA
- Length
- 351 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophosphoesterase; DNA (5'-D(*CP*CP*TP*GP*T)-3')
- UniProt
- A3DJ38
- Ligands
- GTP, MG
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallophosphoesterase | protein | 171 | 51% helix, 22% strand | A3DJ38 |
| C | DNA (5'-D(*CP*CP*TP*GP*T)-3') | dna | 5 | — | — |
| D | DNA (5'-D(*CP*CP*TP*GP*T)-3') | dna | 4 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.62 | 0.83 | 20 | empty |
| 2 | 96 | 0.41 | 0.77 | 17 | empty |
| 3 | 71 | 0.39 | 0.80 | 22 | GTP, MG |
| 4 | 66 | 0.37 | 0.79 | 15 | empty |
| 5 | 79 | 0.36 | 0.77 | 23 | GTP, MG |
Interfaces
3 interfaces between chains.
- A–B · 854 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 678 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 654 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 4MDF · Structure of bacterial polynucleotide kinase Michaelis complex bound to GTP and DNA · 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 A3DJ38
- Elsewhere: RCSB PDB 4MDF · PDBe 4MDF · UniProt A3DJ38
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