MolNFT v1 · #51665 · protein + DNA
Xray structure of kops bound gamma domain of ftsk (P. aeruginosa)
2VE9 · DNA translocase ftsk: “Xray structure of kops bound gamma domain of ftsk (P. aeruginosa)”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.73). MolNFT v1 #51665 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2VE9
- Type
- protein + DNA
- Length
- 432 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA translocase ftsk; 5'-D(*AP*CP*CP*AP*GP*GP*GP*CP*AP*GP *GP*GP*CP*GP*AP*C)-3'…
- UniProt
- Q9I0M3
- Ligands
- MG
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA translocase ftsk | protein | 62 | 52% helix, 3% strand | Q9I0M3 |
| B | DNA translocase ftsk | protein | 61 | 52% helix, 3% strand | Q9I0M3 |
| D, E | DNA translocase ftsk | protein | 62 | 52% helix, 3% strand | Q9I0M3 |
| F | DNA translocase ftsk | protein | 63 | 51% helix, 3% strand | Q9I0M3 |
| I, K | 5'-D(*AP*CP*CP*AP*GP*GP*GP*CP*AP*GP *GP*GP*CP*GP*AP*C)-3' | dna | 14 | — | — |
| J, L | 5'-D(*GP*TP*CP*GP*CP*CP*CP*TP*GP*CP *CP*CP*TP*GP*GP*T)-3' | dna | 16 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.73 | 0.93 | 29 | empty |
| 2 | 147 | 0.70 | 0.90 | 32 | empty |
| 3 | 435 | 0.60 | 0.76 | 47 | empty |
| 4 | 253 | 0.52 | 0.76 | 33 | empty |
| 5 | 169 | 0.43 | 0.75 | 18 | empty |
Interfaces
23 interfaces between chains.
- K–L · 638 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- I–J · 633 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–J · 373 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–J · 368 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–L · 364 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
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 Q9I0M3
- Elsewhere: RCSB PDB 2VE9 · PDBe 2VE9 · UniProt Q9I0M3
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