MolNFT v1 · #155765 · protein
Localized reconstruction of coxsackievirus A16 mature virion in complex with Fab 18A7
6LHT · Light chain variable region of Fab 18A7: “Localized reconstruction of coxsackievirus A16 mature virion in complex with Fab 18A7”. Electron microscopy, 1 ligand (SPH), 18 pockets (best druggability 0.81). MolNFT v1 #155765 on…
- PDB
- 6LHT
- Type
- protein
- Length
- 1,329 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain variable region of Fab 18A7; Heavy chain variable region of Fab 18A7; VP1…
- UniProt
- A0A2S1BJ89
- Ligands
- SPH
- Pockets
- 18 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 7% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain variable region of Fab 18A7 | protein | 113 | 0% helix, 8% strand | — |
| H | Heavy chain variable region of Fab 18A7 | protein | 120 | 0% helix, 19% strand | — |
| A, C | VP1 protein | protein | 218 | 10% helix, 32% strand | A0A2S1BJ89 |
| D, E, B | VP1 protein | protein | 220 | 10% helix, 32% strand | A0A2S1BJ89 |
Ligands and binding sites
- SPH · Sphingosine · ligand · 5 copies · chains A, C, D, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.81 | 0.82 | 73 | empty |
| 2 | 495 | 0.79 | 0.86 | 52 | SPH |
| 3 | 473 | 0.78 | 0.86 | 54 | SPH |
| 4 | 506 | 0.78 | 0.85 | 55 | SPH |
| 5 | 483 | 0.77 | 0.85 | 54 | SPH |
Interfaces
13 interfaces between chains.
- L–H · 1197 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 963 Ų buried · 12 hydrogen bonds · protein-protein
- C–B · 961 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 954 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 948 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6LHT · Localized reconstruction of coxsackievirus A16 mature virion in complex with Fab 18A7 · the same entry in another collection · chain L against L, 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 A0A2S1BJ89
- Elsewhere: RCSB PDB 6LHT · PDBe 6LHT · UniProt A0A2S1BJ89
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