MolNFT v1 · #152550 · protein
Cryo-EM structure of echovirus 6 complexed with its uncoating receptor fcrn at pH 7.4
6ILM · Capsid protein VP1: “Cryo-EM structure of echovirus 6 complexed with its uncoating receptor fcrn at pH 7.4”. Electron microscopy, 3 ligands (SPH, K, NA), 17 pockets (best druggability 0.82). MolNFT v1 #152550 on GenesisL1: 3D…
- PDB
- 6ILM
- Type
- protein
- Length
- 1,202 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
- Ligands
- SPH, K, NA
- Pockets
- 17 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 289 | 7% helix, 28% strand | — |
| B | Capsid protein VP2 | protein | 252 | 9% helix, 34% strand | — |
| C | Capsid protein VP3 | protein | 238 | 5% helix, 28% strand | — |
| D | Capsid protein VP4 | protein | 61 | 5% helix, 15% strand | — |
| E | IgG receptor fcrn large subunit P51 | protein | 263 | 18% helix, 35% strand | P55899 |
| F | Beta-2-microglobulin | protein | 99 | 0% helix, 47% strand | P61769 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
- K · Potassium ion · metal · chains A
- NA · Sodium ion · metal · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.82 | 0.85 | 102 | SPH |
| 2 | 116 | 0.79 | 0.98 | 22 | empty |
| 3 | 487 | 0.68 | 0.79 | 57 | empty |
| 4 | 317 | 0.62 | 0.79 | 47 | empty |
| 5 | 198 | 0.60 | 0.82 | 32 | empty |
Interfaces
10 interfaces between chains.
- A–C · 4265 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2122 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1679 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1610 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1509 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ILM · Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4 · 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 0.97
- 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 6ILM · PDBe 6ILM · UniProt P55899 · UniProt P61769
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