MolNFT v1 · #166143 · protein
Structure of the EVA71 strain 11316 capsid
6UH1 · VP1: “Structure of the EVA71 strain 11316 capsid”. Electron microscopy, 1 ligand (SPH), 14 pockets (best druggability 0.82). MolNFT v1 #166143 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6UH1
- Type
- protein
- Length
- 842 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- D4QGA8, I6W7A3, A0A0E3SXU7, E9RGA0
- Ligands
- SPH
- Pockets
- 14 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 9% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 297 | 7% helix, 28% strand | D4QGA8 |
| B | VP2 | protein | 245 | 11% helix, 33% strand | I6W7A3 |
| C | VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 242 | 8% helix, 31% strand | A0A0E3SXU7 |
| D | VP4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 58 | 10% helix, 9% strand | E9RGA0 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.82 | 0.89 | 64 | SPH |
| 2 | 199 | 0.55 | 0.80 | 37 | empty |
| 3 | 112 | 0.48 | 0.80 | 21 | empty |
| 4 | 176 | 0.48 | 0.77 | 25 | empty |
| 5 | 192 | 0.47 | 0.75 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3934 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2750 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 1725 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1529 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1077 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6UH1 · Structure of the EVA71 strain 11316 capsid · the same entry in another collection · chain D against D, 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 D4QGA8
- Every structure of UniProt I6W7A3
- Every structure of UniProt A0A0E3SXU7
- Every structure of UniProt E9RGA0
- Elsewhere: RCSB PDB 6UH1 · PDBe 6UH1 · UniProt D4QGA8 · UniProt I6W7A3 · UniProt A0A0E3SXU7 · UniProt E9RGA0
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