MolNFT v1 · #152483 · protein + RNA
Crystal structure of a standalone versatile eal protein from vibrio cholerae O395 - 5'-pgpg bound form
6IJ2 · Eal domain protein: “Crystal structure of a standalone versatile eal protein from vibrio cholerae O395 - 5'-pgpg bound form”. X-ray diffraction, 1 ligand (CA), 11 pockets (best druggability 0.70). MolNFT v1 #152483 on GenesisL1: 3D…
- PDB
- 6IJ2
- Type
- protein + RNA
- Length
- 952 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eal domain protein; RNA (5'-R(P*GP*G)-3')
- UniProt
- A0A0H3AJ04
- Ligands
- CA
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Eal domain protein | protein | 236 | 38% helix, 21% strand | A0A0H3AJ04 |
| E, F, G, H | RNA (5'-R(P*GP*G)-3') | rna | 2 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.70 | 0.79 | 57 | empty |
| 2 | 129 | 0.67 | 0.89 | 20 | empty |
| 3 | 87 | 0.66 | 0.91 | 17 | empty |
| 4 | 326 | 0.57 | 0.76 | 47 | empty |
| 5 | 233 | 0.57 | 0.79 | 38 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1188 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1171 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 505 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–H · 505 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6IJ2 · Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395… · 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 A0A0H3AJ04
- Elsewhere: RCSB PDB 6IJ2 · PDBe 6IJ2 · UniProt A0A0H3AJ04
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