Research workbench
Crystal structure of NEU5GC bound pltc
Analyse Crystal structure of NEU5GC bound pltc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EE5
- Type
- protein
- Length
- 599 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
- NGC, GLC, GAL
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Subtilase cytotoxin subunit B-like protein | protein | 118 | 17% helix, 49% strand | A0A716TY65 |
| C | Subtilase cytotoxin subunit B-like protein | protein | 124 | 16% helix, 40% strand | A0A716TY65 |
| D | Subtilase cytotoxin subunit B-like protein | protein | 119 | 17% helix, 40% strand | A0A716TY65 |
| E | Subtilase cytotoxin subunit B-like protein | protein | 120 | 17% helix, 42% strand | A0A716TY65 |
Ligands and binding sites
- NGC · N-glycolyl-alpha-neuraminic acid · sugar · 4 copies · chains A, E, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, E
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, E
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, A
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 | 695 | 0.66 | 0.75 | 31 | empty |
| 2 | 57 | 0.43 | 0.82 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1158 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1082 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1074 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 1063 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1062 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7EE5 · Crystal structure of Neu5Gc 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 7EE5 · PDBe 7EE5 · UniProt A0A716TY65
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