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Crystal structure of E. COLI RNA 3' cyclase
Analyse Crystal structure of E. COLI RNA 3' cyclase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KGD
- Type
- protein
- Length
- 1,356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA 3'-terminal phosphate cyclase
- EC
- 6.5.1.4
- UniProt
- P46849
- Ligands
- AMP, NA, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) | protein | 336 | 33% helix, 31% strand | P46849 |
| B | RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) | protein | 342 | 32% helix, 30% strand | P46849 |
| C | RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) | protein | 338 | 34% helix, 30% strand | P46849 |
| D | RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) | protein | 340 | 33% helix, 29% strand | P46849 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 10 copies · chains A, C, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.82 | 0.83 | 101 | GOL |
| 2 | 935 | 0.79 | 0.82 | 118 | AMP, GOL, NA, SO4 |
| 3 | 100 | 0.78 | 0.98 | 26 | empty |
| 4 | 86 | 0.77 | 0.99 | 24 | empty |
| 5 | 85 | 0.76 | 0.98 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 499 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 372 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 322 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 314 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
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 P46849
- Elsewhere: RCSB PDB 3KGD · PDBe 3KGD · UniProt P46849
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