Research workbench
Cryo-EM structure of archaeal extremophilic internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) at 3.74 Angstroms resolution.
Analyse Cryo-EM structure of archaeal extremophilic internal membrane-containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H9C
- Type
- protein
- Length
- 5,703 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.74
- Source
- Haloarcula californiae ATCC 33799
- Molecule
- VP7; VP9; GPS-III molecule located underneath the capsomer close to the icosahedral…
- UniProt
- A0A1C7A3R1, A0A1C7A3R7, A0A1C7A3R2
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.74 · 10 distinct chains · 13% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F, E, R, S, W, J | VP7 | protein | 174 | 8% helix, 32% strand | A0A1C7A3R1 |
| b | VP9 | protein | 131 | 18% helix, 21% strand | A0A1C7A3R7 |
| c | GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis. | protein | 108 | 15% helix, 30% strand | — |
| d | GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis. | protein | 75 | 59% helix, 0% strand | — |
| e | (Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis. | protein | 46 | 59% helix, 0% strand | — |
| f | Peripentonal unknown polypeptide | protein | 18 | 61% helix, 0% strand | — |
| Z, A, B, C, P, Q, O, V, U, H, G, X | VP4 | protein | 229 | 4% helix, 30% strand | A0A1C7A3R2 |
| T, K, N, a | VP7 | protein | 172 | 7% helix, 32% strand | A0A1C7A3R1 |
| M | VP7 | protein | 170 | 2% helix, 31% strand | A0A1C7A3R1 |
| I, L, Y | VP7 | protein | 167 | 7% helix, 34% strand | A0A1C7A3R1 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.84 | 0.86 | 121 | empty |
| 2 | 831 | 0.81 | 0.84 | 112 | empty |
| 3 | 700 | 0.79 | 0.83 | 91 | empty |
| 4 | 199 | 0.77 | 0.91 | 36 | empty |
| 5 | 985 | 0.76 | 0.78 | 63 | empty |
Interfaces
68 interfaces between chains.
- V–W · 1645 Ų buried · 28 hydrogen bonds · protein-protein
- P–R · 1610 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 1599 Ų buried · 24 hydrogen bonds · protein-protein
- Q–T · 1411 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 1408 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6H9C · Cryo-EM structure of archaeal extremophilic internal membrane- containing haloarcula… · the same entry in another collection · chain B against B, 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 A0A1C7A3R1
- Every structure of UniProt A0A1C7A3R7
- Every structure of UniProt A0A1C7A3R2
- Elsewhere: RCSB PDB 6H9C · PDBe 6H9C · UniProt A0A1C7A3R1 · UniProt A0A1C7A3R7 · UniProt A0A1C7A3R2
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