MolNFT v1 · #162568 · protein
Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant in complex with sialic acid
6RD1 · Putative N-acetylneuraminate lyase: “Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant in complex with sialic acid”. X-ray diffraction, 1 ligand (SI3), 6 pockets (best druggability 0.67). MolNFT v1 #162568 on…
- 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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