MolNFT v1 · #155761 · protein
The cryo-EM structure of coxsackievirus A16 mature virion in complex with Fab 14B10
6LHP · Light chain variable region of Fab 14B10: “The cryo-EM structure of coxsackievirus A16 mature virion in complex with Fab 14B10”. Electron microscopy, 1 ligand (SPH), 20 pockets (best druggability 0.85). MolNFT v1 #155761 on…
- PDB
- 6LHP
- Type
- protein
- Length
- 1,045 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain variable region of Fab 14B10; Heavy chain variable region of Fab 14B10; VP1…
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- A0A2S1BJ89, A0A1D3TZV2, A0A2R4NBT3, A5HX42
- Ligands
- SPH
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain variable region of Fab 14B10 | protein | 101 | 0% helix, 29% strand | — |
| H | Heavy chain variable region of Fab 14B10 | protein | 115 | 3% helix, 50% strand | — |
| A | VP1 protein | protein | 284 | 10% helix, 27% strand | A0A2S1BJ89 |
| B | VP2 protein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 245 | 8% helix, 33% strand | A0A1D3TZV2 |
| C | VP3 protein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 242 | 11% helix, 33% strand | A0A2R4NBT3 |
| D | VP4 protein | protein | 58 | 12% helix, 3% strand | A5HX42 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.85 | 0.90 | 72 | SPH |
| 2 | 73 | 0.61 | 0.90 | 22 | empty |
| 3 | 52 | 0.61 | 0.93 | 20 | empty |
| 4 | 276 | 0.58 | 0.78 | 42 | empty |
| 5 | 137 | 0.46 | 0.78 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–C · 3969 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2407 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1689 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1579 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1052 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6LHP · The cryo-EM structure of coxsackievirus A16 mature virion in complex with Fab 14B10 · 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
- Every structure of UniProt A0A1D3TZV2
- Every structure of UniProt A0A2R4NBT3
- Every structure of UniProt A5HX42
- Elsewhere: RCSB PDB 6LHP · PDBe 6LHP · UniProt A0A2S1BJ89 · UniProt A0A1D3TZV2 · UniProt A0A2R4NBT3 · UniProt A5HX42
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