Research workbench
Crystal structure of NEU5AC bound pltc
Analyse Crystal structure of NEU5AC bound pltc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EE4
- Type
- protein
- Length
- 596 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilase cytotoxin subunit B-like protein
- UniProt
- A0A716TY65
- Ligands
- SIA, GAL, GLC
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Subtilase cytotoxin subunit B-like protein | protein | 118 | 17% helix, 45% strand | A0A716TY65 |
| C | Subtilase cytotoxin subunit B-like protein | protein | 124 | 16% helix, 40% strand | A0A716TY65 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, D, E
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.67 | 0.75 | 30 | empty |
| 2 | 57 | 0.42 | 0.81 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–E · 1150 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1070 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1066 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1065 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 1064 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7EE4 · Crystal structure of Neu5Ac bound PltC · 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 A0A716TY65
- Elsewhere: RCSB PDB 7EE4 · PDBe 7EE4 · UniProt A0A716TY65
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