MolNFT v1 · #24257 · protein
Recombinant vanadium-dependent bromoperoxidase from red algae corallina pilulifera
1UP8 · Vanadium-dependent bromoperoxidase 1: “Recombinant vanadium-dependent bromoperoxidase from red algae corallina pilulifera”. X-ray diffraction, 2 ligands (CA, PO4), 20 pockets (best druggability 0.81). MolNFT v1 #24257 on GenesisL1…
- PDB
- 1UP8
- Type
- protein
- Length
- 2,388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vanadium-dependent bromoperoxidase 1
- UniProt
- O81959
- Ligands
- CA, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Vanadium-dependent bromoperoxidase 1 | protein | 597 | 44% helix, 10% strand | O81959 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 940 | 0.81 | 0.83 | 88 | PO4 |
| 2 | 1008 | 0.79 | 0.81 | 86 | empty |
| 3 | 945 | 0.79 | 0.81 | 70 | PO4 |
| 4 | 992 | 0.78 | 0.80 | 68 | PO4 |
| 5 | 973 | 0.78 | 0.80 | 69 | PO4 |
Interfaces
6 interfaces between chains.
- C–D · 5451 Ų buried · 98 hydrogen bonds · protein-protein
- A–B · 5418 Ų buried · 102 hydrogen bonds · protein-protein
- A–C · 986 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 560 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 178 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1UP8 · Recombinant vanadium-dependent bromoperoxidase from red algae Corallina pilulifera · the same entry in another collection · chain A against A, TM-score 1.00
- O81959 · AlphaFold monomer V2.0 prediction for vanadium-dependent bromoperoxidase (O81959) · a predicted model of the same protein · 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 O81959
- Elsewhere: RCSB PDB 1UP8 · PDBe 1UP8 · UniProt O81959
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