Research workbench
Cryo-EM structure of echovirus 11 complexed with its uncoating receptor fcrn at pH 5.5
Analyse Cryo-EM structure of echovirus 11 complexed with its uncoating receptor fcrn at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LA7
- Type
- protein
- Length
- 1,195 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4; IgG…
- UniProt
- P55899, P61769
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 6 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 285 | 9% helix, 32% strand | — |
| B | Capsid protein VP2 | protein | 251 | 7% helix, 36% strand | — |
| C | Capsid protein VP3 | protein | 238 | 8% helix, 29% strand | — |
| D | Capsid protein VP4 | protein | 59 | 12% helix, 17% strand | — |
| E | IgG receptor fcrn large subunit P51 | protein | 263 | 21% helix, 37% strand | P55899 |
| F | Beta-2-microglobulin | protein | 99 | 0% helix, 44% strand | P61769 |
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 | 746 | 0.77 | 0.82 | 87 | empty |
| 2 | 464 | 0.77 | 0.85 | 76 | empty |
| 3 | 428 | 0.63 | 0.77 | 42 | empty |
| 4 | 249 | 0.61 | 0.80 | 33 | empty |
| 5 | 59 | 0.60 | 0.91 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–C · 4417 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 2068 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1538 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1470 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1423 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6LA7 · Cryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 5.5 · the same entry in another collection · chain F against F, TM-score 1.00
- P55899 · AlphaFold monomer V2.0 prediction for IgG receptor fcrn large subunit P51 (P55899) · a predicted model of the same protein · chain E against A, TM-score 0.96
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 P55899
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6LA7 · PDBe 6LA7 · UniProt P55899 · UniProt P61769
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