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Structure from the mobile metagenome of V.CHOLERAE. integron cassette protein VCH_CASS6
Analyse Structure from the mobile metagenome of V.CHOLERAE. integron cassette protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I9S
- Type
- protein
- Length
- 644 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integron cassette protein
- Ligands
- SO4, CL
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integron cassette protein | protein | 161 | 45% helix, 31% strand | — |
| B | Integron cassette protein | protein | 162 | 43% helix, 31% strand | — |
| C | Integron cassette protein | protein | 161 | 43% helix, 32% strand | — |
| D | Integron cassette protein | protein | 160 | 44% helix, 31% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.77 | 0.80 | 92 | SO4 |
| 2 | 374 | 0.68 | 0.81 | 41 | CL |
| 3 | 426 | 0.66 | 0.79 | 47 | SO4, CL |
| 4 | 370 | 0.66 | 0.80 | 42 | empty |
| 5 | 384 | 0.64 | 0.78 | 44 | CL |
Interfaces
6 interfaces between chains.
- C–D · 3671 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 3642 Ų buried · 61 hydrogen bonds · protein-protein
- B–D · 695 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 598 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 281 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3I9S · Structure from the mobile metagenome of V.cholerae. Integron cassette protein VCH_CASS6 · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 3I9S · PDBe 3I9S
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