Research workbench
Crystal structure of rida from antarctic bacterium psychrobacter sp. pamc 21119
Analyse Crystal structure of rida from antarctic bacterium psychrobacter sp. pamc 21119 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L8P
- Type
- protein
- Length
- 371 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rida family protein
- UniProt
- A0A2N5LLK3
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Rida family protein | protein | 124 | 31% helix, 32% strand | A0A2N5LLK3 |
| B | Rida family protein | protein | 123 | 31% helix, 33% strand | A0A2N5LLK3 |
Ligands and binding sites
- MLI · Malonate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.81 | 0.97 | 38 | empty |
| 2 | 128 | 0.47 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1010 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 998 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 979 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6L8P · Crystal structure of RidA from Antarctic bacterium Psychrobacter sp. PAMC 21119 · 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 A0A2N5LLK3
- Elsewhere: RCSB PDB 6L8P · PDBe 6L8P · UniProt A0A2N5LLK3
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