Research workbench
Deoxyguanosinetriphosphate triphosphohydrolase from escherichia COLI with two DNA effector molecules
Analyse Deoxyguanosinetriphosphate triphosphohydrolase from escherichia COLI with two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X9E
- Type
- protein + RNA
- Length
- 2,994 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyguanosinetriphosphate triphosphohydrolase; RNA (5'-R(P*CP*CP*C)-3')
- EC
- 3.1.5.1
- UniProt
- P15723
- Ligands
- MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 64% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 499 | 65% helix, 2% strand | P15723 |
| B | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 495 | 64% helix, 2% strand | P15723 |
| C | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 500 | 64% helix, 2% strand | P15723 |
| D | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 501 | 64% helix, 2% strand | P15723 |
| E | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 496 | 65% helix, 2% strand | P15723 |
| F | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 497 | 64% helix, 2% strand | P15723 |
| G, H | RNA (5'-R(P*CP*CP*C)-3') | rna | 3 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.81 | 0.87 | 80 | empty |
| 2 | 970 | 0.81 | 0.82 | 98 | empty |
| 3 | 779 | 0.75 | 0.80 | 70 | empty |
| 4 | 587 | 0.75 | 0.82 | 50 | empty |
| 5 | 931 | 0.75 | 0.78 | 73 | MG |
Interfaces
16 interfaces between chains.
- C–D · 2155 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1840 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1821 Ų buried · 28 hydrogen bonds · protein-protein
- C–E · 785 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 746 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4X9E · DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE from Escherichia coli with two DNA… · the same entry in another collection · chain H against H, TM-score 1.00
- P15723 · AlphaFold monomer V2.0 prediction for deoxyguanosinetriphosphate triphosphohydrolase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P15723
- Elsewhere: RCSB PDB 4X9E · PDBe 4X9E · UniProt P15723
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