Research workbench
Cryo-EM structure of the archaeal extremophilic internal membrane containing haloarcula hispanica icosahedral virus 2 (hhiv-2) at 3.78 ångströms resolution.
Analyse Cryo-EM structure of the 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
- 6H82
- Type
- protein
- Length
- 5,906 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP4; VP7; Uncharacterized protein; VP16 (vertex complex); Gps III; Polypeptide stretch…
- UniProt
- H9AZX2, H9AZX1, H9AZX8
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 8 distinct chains · 4% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, Q, P, O, U, Z, V, H, G, X | VP4 | protein | 229 | 3% helix, 37% strand | H9AZX2 |
| D, T, J, W | VP7 | protein | 172 | 2% helix, 36% strand | H9AZX1 |
| E, F, R, S, K, M, N, a | VP7 | protein | 175 | 4% helix, 34% strand | H9AZX1 |
| L, I, Y | VP7 | protein | 161 | 0% helix, 37% strand | H9AZX1 |
| b | Uncharacterized protein | protein | 135 | 8% helix, 42% strand | H9AZX8 |
| g | VP16 (vertex complex) | protein | 217 | 1% helix, 19% strand | — |
| c, d | Gps III | protein | 105 | 15% helix, 28% strand | — |
| m | Polypeptide stretch (vertex complex) | protein | 25 | 12% helix, 8% strand | — |
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 | 486 | 0.83 | 0.90 | 65 | empty |
| 2 | 642 | 0.83 | 0.88 | 71 | empty |
| 3 | 1006 | 0.80 | 0.82 | 116 | empty |
| 4 | 838 | 0.80 | 0.83 | 115 | empty |
| 5 | 1002 | 0.79 | 0.81 | 113 | empty |
Interfaces
66 interfaces between chains.
- V–W · 1454 Ų buried · 21 hydrogen bonds · protein-protein
- P–R · 1393 Ų buried · 17 hydrogen bonds · protein-protein
- X–a · 1352 Ų buried · 20 hydrogen bonds · protein-protein
- Z–K · 1352 Ų buried · 20 hydrogen bonds · protein-protein
- Q–T · 1348 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6H82 · Cryo-EM structure of the archaeal extremophilic internal membrane containing Haloarcula… · 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 H9AZX2
- Every structure of UniProt H9AZX1
- Every structure of UniProt H9AZX8
- Elsewhere: RCSB PDB 6H82 · PDBe 6H82 · UniProt H9AZX2 · UniProt H9AZX1 · UniProt H9AZX8
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