Research workbench
Pnp-tmp bound oligoribonuclease (orn) from colwellia psychrerythraea strain 34H
Analyse Pnp-tmp bound oligoribonuclease (orn) from colwellia psychrerythraea strain 34H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A4D
- Type
- protein
- Length
- 366 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligoribonuclease
- EC
- 3.1.-.-
- UniProt
- Q47VZ4
- Ligands
- 9RC
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligoribonuclease (EC 3.1.-.-) | protein | 184 | 48% helix, 16% strand | Q47VZ4 |
| B | Oligoribonuclease (EC 3.1.-.-) | protein | 182 | 48% helix, 16% strand | Q47VZ4 |
Ligands and binding sites
- 9RC · 5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.75 | 0.78 | 103 | 9RC |
Interfaces
1 interface between chains.
- A–B · 1607 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6A4D · pNP-TMP bound Oligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H · the same entry in another collection · chain A against A, TM-score 1.00
- Q47VZ4 · AlphaFold monomer V2.0 prediction for oligoribonuclease (Q47VZ4) · 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 Q47VZ4
- Elsewhere: RCSB PDB 6A4D · PDBe 6A4D · UniProt Q47VZ4
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