Research workbench
Membrane-embedded monofunctional glycosyltransferase waaa of aquifex aeolicus, substrate-free form
Analyse Membrane-embedded monofunctional glycosyltransferase waaa of aquifex aeolicus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XCI
- Type
- protein
- Length
- 1,411 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-manno-2-octulosonic acid transferase
- UniProt
- O66663
- Ligands
- NI, CL
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-manno-2-octulosonic acid transferase | protein | 354 | 44% helix, 18% strand | O66663 |
| B, D | 3-deoxy-D-manno-2-octulosonic acid transferase | protein | 352 | 45% helix, 18% strand | O66663 |
| C | 3-deoxy-D-manno-2-octulosonic acid transferase | protein | 353 | 46% helix, 18% strand | O66663 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, D
- GOL · Glycerol · additive · 8 copies · chains A, C, B, D
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, C, B, D
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.78 | 0.81 | 81 | PG4, GOL |
| 2 | 763 | 0.74 | 0.79 | 61 | GOL, PG4 |
| 3 | 249 | 0.55 | 0.77 | 40 | empty |
| 4 | 146 | 0.51 | 0.79 | 31 | GOL |
| 5 | 236 | 0.51 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1330 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1145 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 207 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2XCI · Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus… · the same entry in another collection · chain A against A, TM-score 1.00
- O66663 · AlphaFold monomer V2.0 prediction for 3-deoxy-D-manno-octulosonic acid transferase… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O66663
- Elsewhere: RCSB PDB 2XCI · PDBe 2XCI · UniProt O66663
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