Research workbench
A three-gate structure of topoisomerase IV from streptococcus pneumoniae
Analyse A three-gate structure of topoisomerase IV from streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I3H
- Type
- protein + DNA
- Length
- 2,140 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP*…
- EC
- 5.99.1.-, 5.99.1.3
- UniProt
- Q3HZ71, D6ZLV0
- Ligands
- MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'- D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP* CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3') | dna | 14 | — | — |
| F | DNA (5'- D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP* TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3') | dna | 14 | — | — |
| A | Topoisomerase IV subunit B, DNA topoisomerase 4 subunit a chimera (EC 5.99.1.-, 5.99.1.3) | protein | 1037 | 42% helix, 19% strand | Q3HZ71, D6ZLV0 |
| B | Topoisomerase IV subunit B, DNA topoisomerase 4 subunit a chimera (EC 5.99.1.-, 5.99.1.3) | protein | 1035 | 43% helix, 19% strand | Q3HZ71, D6ZLV0 |
| G | DNA (5'- D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP* CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3') | dna | 20 | — | — |
| H | DNA (5'- D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP* TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3') | dna | 20 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.78 | 0.83 | 66 | empty |
| 2 | 1084 | 0.76 | 0.78 | 115 | empty |
| 3 | 498 | 0.74 | 0.83 | 39 | MG |
| 4 | 557 | 0.73 | 0.81 | 74 | empty |
| 5 | 625 | 0.72 | 0.79 | 77 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3435 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 902 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- B–G · 858 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–H · 857 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–H · 780 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 4I3H · A three-gate structure of topoisomerase IV from Streptococcus pneumoniae · the same entry in another collection · chain E against E, 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 Q3HZ71
- Every structure of UniProt D6ZLV0
- Elsewhere: RCSB PDB 4I3H · PDBe 4I3H · UniProt Q3HZ71 · UniProt D6ZLV0
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