MolNFT v1 · #115927 · protein
Crystal structure of an oligoribonuclease from acinetobacter baumannii
5CY4: “Crystal structure of an oligoribonuclease from acinetobacter baumannii”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.84). MolNFT v1 #115927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CY4
- Type
- protein
- Length
- 1,089 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligoribonuclease
- EC
- 3.1.-.-
- UniProt
- V5VGJ9
- Ligands
- CA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligoribonuclease (EC 3.1.-.-) | protein | 182 | 47% helix, 18% strand | V5VGJ9 |
| B | Oligoribonuclease (EC 3.1.-.-) | protein | 177 | 46% helix, 18% strand | V5VGJ9 |
| C | Oligoribonuclease (EC 3.1.-.-) | protein | 184 | 46% helix, 17% strand | V5VGJ9 |
| D | Oligoribonuclease (EC 3.1.-.-) | protein | 184 | 46% helix, 17% strand | V5VGJ9 |
| E | Oligoribonuclease (EC 3.1.-.-) | protein | 180 | 48% helix, 18% strand | V5VGJ9 |
| F | Oligoribonuclease (EC 3.1.-.-) | protein | 182 | 46% helix, 18% strand | V5VGJ9 |
Ligands and binding sites
- CA · Calcium ion · metal · 14 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.84 | 0.86 | 81 | empty |
| 2 | 478 | 0.77 | 0.86 | 54 | CA |
| 3 | 1027 | 0.76 | 0.78 | 76 | CA, EDO |
| 4 | 618 | 0.68 | 0.77 | 53 | CA |
| 5 | 475 | 0.63 | 0.76 | 50 | CA |
Interfaces
8 interfaces between chains.
- C–D · 1696 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1693 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1622 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 582 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 312 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5CY4 · Crystal structure of an oligoribonuclease from Acinetobacter baumannii · 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 V5VGJ9
- Elsewhere: RCSB PDB 5CY4 · PDBe 5CY4 · UniProt V5VGJ9
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