Research workbench
Initial crystallographic structural analysis of a putative HAD/COF-like hydrolase from plasmodium vivax
Analyse Initial crystallographic structural analysis of a putative HAD/COF-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B30
- Type
- protein
- Length
- 1,136 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pvivax hypothetical protein
- UniProt
- A5K063
- Ligands
- CA, CL
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pvivax hypothetical protein | protein | 284 | 39% helix, 21% strand | A5K063 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.76 | 0.80 | 80 | empty |
| 2 | 626 | 0.76 | 0.82 | 59 | empty |
| 3 | 213 | 0.72 | 0.88 | 34 | CA, CL |
| 4 | 227 | 0.71 | 0.87 | 32 | CA, CL |
| 5 | 731 | 0.71 | 0.77 | 47 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1003 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 786 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 702 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2B30 · Initial Crystallographic Structural Analysis of a putative HAD/COF-like hydrolase from… · 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
- Every structure of UniProt A5K063
- Elsewhere: RCSB PDB 2B30 · PDBe 2B30 · UniProt A5K063
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