Research workbench
Structural analysis of the sialyltransferase cstii from campylobacter jejuni in complex with a substrate analogue, cmp-3FNEUAC.
Analyse Structural analysis of the sialyltransferase cstii from campylobacter jejuni in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RO7
- Type
- protein
- Length
- 976 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-2,3/8-sialyltransferase
- EC
- 2.4.99.-
- UniProt
- Q9LAK3
- Ligands
- CSF
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-2,3/8-sialyltransferase (EC 2.4.99.-) | protein | 258 | 39% helix, 16% strand | Q9LAK3 |
| B | Alpha-2,3/8-sialyltransferase (EC 2.4.99.-) | protein | 237 | 43% helix, 16% strand | Q9LAK3 |
| C | Alpha-2,3/8-sialyltransferase (EC 2.4.99.-) | protein | 243 | 40% helix, 17% strand | Q9LAK3 |
| D | Alpha-2,3/8-sialyltransferase (EC 2.4.99.-) | protein | 238 | 44% helix, 17% strand | Q9LAK3 |
Ligands and binding sites
- CSF · Cytidine-5'-monophosphate-3-fluoro-N-acetyl-neuraminic acid · ligand · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.75 | 0.84 | 44 | CSF |
| 2 | 269 | 0.63 | 0.80 | 37 | CSF |
| 3 | 361 | 0.60 | 0.77 | 51 | CSF |
| 4 | 173 | 0.47 | 0.76 | 29 | CSF |
| 5 | 76 | 0.40 | 0.79 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–C · 785 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 780 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 753 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 741 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1RO7 · Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex… · 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 Q9LAK3
- Elsewhere: RCSB PDB 1RO7 · PDBe 1RO7 · UniProt Q9LAK3
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