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Crystal structure of exodeoxyribonuclease VII small subunit (NP_881400.1) from bordetella pertussis at 2.40 a resolution
Analyse Crystal structure of exodeoxyribonuclease VII small subunit (NP_881400.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VP7
- Type
- protein
- Length
- 417 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease VII small subunit
- EC
- 3.1.11.6
- UniProt
- Q7W7Q2
- Pockets
- 5 · best druggability 0.40
Structure
x-ray diffraction · 6 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease VII small subunit (EC 3.1.11.6) | protein | 68 | 78% helix, 1% strand | Q7W7Q2 |
| B | Exodeoxyribonuclease VII small subunit (EC 3.1.11.6) | protein | 77 | 71% helix, 1% strand | Q7W7Q2 |
| C | Exodeoxyribonuclease VII small subunit (EC 3.1.11.6) | protein | 71 | 73% helix, 1% strand | Q7W7Q2 |
| D | Exodeoxyribonuclease VII small subunit (EC 3.1.11.6) | protein | 69 | 77% helix, 0% strand | Q7W7Q2 |
| E | Exodeoxyribonuclease VII small subunit (EC 3.1.11.6) | protein | 67 | 79% helix, 1% strand | Q7W7Q2 |
| F | Exodeoxyribonuclease VII small subunit (EC 3.1.11.6) | protein | 65 | 82% helix, 0% strand | Q7W7Q2 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.40 | 0.75 | 16 | empty |
| 2 | 105 | 0.37 | 0.74 | 18 | empty |
| 3 | 93 | 0.33 | 0.73 | 15 | empty |
| 4 | 74 | 0.31 | 0.74 | 19 | empty |
| 5 | 67 | 0.31 | 0.75 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1301 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1188 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1069 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 497 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1VP7 · Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella… · the same entry in another collection · chain F against F, TM-score 1.00
- Q7W7Q2 · AlphaFold monomer V2.0 prediction for exodeoxyribonuclease 7 small subunit (Q7W7Q2) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 Q7W7Q2
- Elsewhere: RCSB PDB 1VP7 · PDBe 1VP7 · UniProt Q7W7Q2
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