MolNFT v1 · #175312 · protein
Pare in complex with amppnp
7CMP · DNA topoisomerase 4 subunit B: “Pare in complex with amppnp”. X-ray diffraction, 2 ligands (ANP, MG), 20 pockets (best druggability 0.81). MolNFT v1 #175312 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CMP
- Type
- protein
- Length
- 1,496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit B
- EC
- 5.6.2.2
- UniProt
- Q5GYJ8
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA topoisomerase 4 subunit B (EC 5.6.2.2) | protein | 374 | 34% helix, 26% strand | Q5GYJ8 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.81 | 0.98 | 33 | MG, ANP |
| 2 | 158 | 0.81 | 0.97 | 36 | MG, ANP |
| 3 | 152 | 0.81 | 0.97 | 38 | MG, ANP |
| 4 | 138 | 0.80 | 0.98 | 32 | MG, ANP |
| 5 | 655 | 0.74 | 0.81 | 66 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2609 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2396 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 165 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 115 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7CMP · parE in complex with AMPPNP · 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 Q5GYJ8
- Elsewhere: RCSB PDB 7CMP · PDBe 7CMP · UniProt Q5GYJ8
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