Research workbench
Crystal structure of E. COLI RNA helicase hrpa in complex with RNA
Analyse Crystal structure of E. COLI RNA helicase hrpa in complex with RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZWW
- Type
- protein + RNA
- Length
- 3,003 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase hrpa; Ssrna
- EC
- 3.6.4.13
- UniProt
- A0A167DLY9
- Ligands
- CA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase hrpa (EC 3.6.4.13) | protein | 744 | 42% helix, 19% strand | A0A167DLY9 |
| C | ATP-dependent RNA helicase hrpa (EC 3.6.4.13) | protein | 749 | 43% helix, 18% strand | A0A167DLY9 |
| E | ATP-dependent RNA helicase hrpa (EC 3.6.4.13) | protein | 731 | 43% helix, 19% strand | A0A167DLY9 |
| G | ATP-dependent RNA helicase hrpa (EC 3.6.4.13) | protein | 735 | 44% helix, 19% strand | A0A167DLY9 |
| B, D | Ssrna | rna | 12 | — | — |
| F, H | Ssrna | rna | 10 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, C, E, G
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 | 1084 | 0.89 | 0.91 | 126 | empty |
| 2 | 1033 | 0.89 | 0.90 | 128 | empty |
| 3 | 1122 | 0.89 | 0.90 | 127 | empty |
| 4 | 225 | 0.79 | 0.93 | 40 | empty |
| 5 | 740 | 0.79 | 0.83 | 73 | empty |
Interfaces
7 interfaces between chains.
- E–G · 2192 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2181 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1607 Ų buried · 37 hydrogen bonds · protein-nucleic
- C–D · 1604 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–B · 1602 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 6ZWW · Crystal structure of E. coli RNA helicase HrpA in complex with RNA · 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 A0A167DLY9
- Elsewhere: RCSB PDB 6ZWW · PDBe 6ZWW · UniProt A0A167DLY9
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