Research workbench
Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant in complex with sialic acid
Analyse Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RD1
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative N-acetylneuraminate lyase
- UniProt
- A7B555
- Ligands
- SI3
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative N-acetylneuraminate lyase | protein | 304 | 53% helix, 13% strand | A7B555 |
Ligands and binding sites
- SI3 · 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.67 | 0.79 | 39 | SI3 |
| 2 | 213 | 0.66 | 0.85 | 43 | empty |
| 3 | 349 | 0.65 | 0.80 | 35 | SI3 |
| 4 | 65 | 0.31 | 0.74 | 16 | empty |
| 5 | 56 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1618 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6RD1 · Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant in complex with sialic… · 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 A7B555
- Elsewhere: RCSB PDB 6RD1 · PDBe 6RD1 · UniProt A7B555
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