Research workbench
Cdt of sidd, deampylase from legionella pneumophila
Analyse Cdt of sidd, deampylase from legionella pneumophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RP4
- Type
- protein
- Length
- 504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine monophosphate-protein hydrolase sidd
- UniProt
- Q6RCR2
- Ligands
- ZN, MG, NA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine monophosphate-protein hydrolase sidd | protein | 125 | 66% helix, 0% strand | Q6RCR2 |
| B | Adenosine monophosphate-protein hydrolase sidd | protein | 127 | 58% helix, 0% strand | Q6RCR2 |
| C | Adenosine monophosphate-protein hydrolase sidd | protein | 124 | 65% helix, 0% strand | Q6RCR2 |
| D | Adenosine monophosphate-protein hydrolase sidd | protein | 128 | 66% helix, 0% strand | Q6RCR2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.79 | 0.80 | 60 | empty |
| 2 | 929 | 0.78 | 0.81 | 68 | GOL |
| 3 | 189 | 0.67 | 0.85 | 28 | empty |
| 4 | 176 | 0.62 | 0.83 | 22 | empty |
| 5 | 250 | 0.59 | 0.79 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 501 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 498 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 419 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 387 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 314 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6RP4 · CDT of SidD, deAMPylase from Legionella pneumophila · 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 Q6RCR2
- Elsewhere: RCSB PDB 6RP4 · PDBe 6RP4 · UniProt Q6RCR2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.