MolNFT v1 · #184948 · protein
Crystal structure of fhit covalently bound to a nucleotide
7P8P · BIS(5'-adenosyl)-triphosphatase: “Crystal structure of fhit covalently bound to a nucleotide”. X-ray diffraction, 2 ligands (6BI, NA), 4 pockets (best druggability 0.78). MolNFT v1 #184948 on GenesisL1: 3D structure, binding sites…
- PDB
- 7P8P
- Type
- protein
- Length
- 541 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BIS(5'-adenosyl)-triphosphatase
- EC
- 3.6.1.29
- UniProt
- P49789
- Ligands
- 6BI, NA
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BIS(5'-adenosyl)-triphosphatase (EC 3.6.1.29) | protein | 128 | 34% helix, 27% strand | P49789 |
| B | BIS(5'-adenosyl)-triphosphatase (EC 3.6.1.29) | protein | 147 | 38% helix, 23% strand | P49789 |
| C | BIS(5'-adenosyl)-triphosphatase (EC 3.6.1.29) | protein | 127 | 35% helix, 27% strand | P49789 |
| D | BIS(5'-adenosyl)-triphosphatase (EC 3.6.1.29) | protein | 139 | 39% helix, 24% strand | P49789 |
Ligands and binding sites
- 6BI · [(2~{R},3~{S},4~{R},5~{R})-5-[6-(ethylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · 4 copies · chains A, C, B, D
- NA · Sodium ion · metal · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.78 | 0.80 | 79 | 6BI, NA, TRS |
| 2 | 221 | 0.60 | 0.81 | 32 | 6BI |
| 3 | 171 | 0.59 | 0.82 | 28 | 6BI, NA |
| 4 | 146 | 0.57 | 0.82 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1292 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1291 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 381 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7P8P · Crystal structure of Fhit covalently bound to a nucleotide · the same entry in another collection · chain A against A, TM-score 1.00
- P49789 · AlphaFold monomer V2.0 prediction for BIS(5'-adenosyl)-triphosphatase (P49789) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P49789
- Elsewhere: RCSB PDB 7P8P · PDBe 7P8P · UniProt P49789
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