Research workbench
Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant
Analyse Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RB7
- Type
- protein
- Length
- 1,220 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative N-acetylneuraminate lyase
- UniProt
- A7B555
- Ligands
- BCN, MG
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Putative N-acetylneuraminate lyase | protein | 305 | 53% helix, 13% strand | A7B555 |
Ligands and binding sites
- BCN · Bicine · ligand · chains A, E
- MG · Magnesium ion · metal · 4 copies · chains A, B, E, F
- GOL · Glycerol · additive · 6 copies · chains A, B, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, E, F
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, E, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.68 | 0.86 | 37 | empty |
| 2 | 230 | 0.68 | 0.85 | 45 | empty |
| 3 | 395 | 0.67 | 0.80 | 38 | TRS, GOL, MG |
| 4 | 381 | 0.67 | 0.80 | 38 | TRS, GOL, MG |
| 5 | 426 | 0.67 | 0.79 | 39 | TRS, GOL, MG |
Interfaces
4 interfaces between chains.
- E–F · 1666 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1664 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1085 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1082 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6RB7 · Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant · 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 6RB7 · PDBe 6RB7 · UniProt A7B555
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