Research workbench
Cryoem structure of mannose transporter manyz and microcin E492 (mcea) complex
Analyse Cryoem structure of mannose transporter manyz and microcin E492 (mcea) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DYR
- Type
- protein
- Length
- 1,791 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pts system mannose-specific eiic component; Pts system mannose-specific eiid component…
- UniProt
- P69801, P69805, Q9Z4N4
- Ligands
- MAN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 69% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, B, E | Pts system mannose-specific eiic component | protein | 248 | 73% helix, 1% strand | P69801 |
| Z, C, F | Pts system mannose-specific eiid component | protein | 274 | 69% helix, 3% strand | P69805 |
| A, D, G | Microcin E492 | protein | 75 | 56% helix, 1% strand | Q9Z4N4 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains Y, Z, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.88 | 0.90 | 45 | empty |
| 2 | 64 | 0.71 | 0.98 | 19 | MAN |
| 3 | 61 | 0.71 | 0.98 | 21 | MAN |
| 4 | 57 | 0.69 | 0.97 | 20 | MAN |
| 5 | 264 | 0.52 | 0.75 | 34 | empty |
Interfaces
24 interfaces between chains.
- E–F · 4996 Ų buried · 34 hydrogen bonds · protein-protein
- Y–Z · 4988 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 4988 Ų buried · 35 hydrogen bonds · protein-protein
- F–G · 1109 Ų buried · 3 hydrogen bonds · protein-protein
- Z–A · 1105 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7DYR · CryoEM Structure of Mannose Transporter ManYZ and Microcin E492 (MceA) complex · the same entry in another collection · chain G against G, TM-score 1.00
- P69805 · AlphaFold monomer V2.0 prediction for pts system mannose-specific eiid component (P69805) · a predicted model of the same protein · chain Z against A, TM-score 0.83
- P69801 · AlphaFold monomer V2.0 prediction for pts system mannose-specific eiic component (P69801) · a predicted model of the same protein · chain Y against A, TM-score 0.66
- Q9Z4N4 · AlphaFold monomer V2.0 prediction for microcin E492 (Q9Z4N4) · a predicted model of the same protein · chain A against A, TM-score 0.58
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 P69801
- Every structure of UniProt P69805
- Every structure of UniProt Q9Z4N4
- Elsewhere: RCSB PDB 7DYR · PDBe 7DYR · UniProt P69801 · UniProt P69805 · UniProt Q9Z4N4
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