Research workbench
Crystal structure of a cupin domain (BP2299) from bordetella pertussis tohama I at 1.80 a resolution
Analyse Crystal structure of a cupin domain (BP2299) from bordetella pertussis tohama I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FQP
- Type
- protein
- Length
- 377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein BP2299
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein BP2299 | protein | 95 | 0% helix, 57% strand | — |
| B | Hypothetical protein BP2299 | protein | 92 | 0% helix, 59% strand | — |
| C | Hypothetical protein BP2299 | protein | 96 | 0% helix, 56% strand | — |
| D | Hypothetical protein BP2299 | protein | 94 | 0% helix, 57% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.61 | 0.74 | 43 | empty |
| 2 | 87 | 0.44 | 0.79 | 25 | ZN, ACT |
| 3 | 64 | 0.41 | 0.81 | 21 | ZN, ACT |
Interfaces
5 interfaces between chains.
- C–D · 921 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 901 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 96 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2FQP · Crystal structure of a cupin domain (bp2299) from bordetella pertussis tohama i at 1.80 A… · the same entry in another collection · chain C against C, 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 2FQP · PDBe 2FQP
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