Research workbench
Human cytosolic 5' nucleotidase iiib in complex with 3,4-dif- BN7GUANINE
Analyse Human cytosolic 5' nucleotidase iiib in complex with 3,4-dif- BN7GUANINE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZEH
- Type
- protein
- Length
- 1,104 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7-methylguanosine phosphate-specific 5'-nucleotidase
- EC
- 3.1.3.91, 3.1.3.5
- UniProt
- Q969T7
- Ligands
- IPQ, RBL, MG, PO4, SO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7-methylguanosine phosphate-specific 5'-nucleotidase (EC 3.1.3.91, 3.1.3.5) | protein | 274 | 46% helix, 21% strand | Q969T7 |
| B | 7-methylguanosine phosphate-specific 5'-nucleotidase (EC 3.1.3.91, 3.1.3.5) | protein | 275 | 44% helix, 21% strand | Q969T7 |
| C | 7-methylguanosine phosphate-specific 5'-nucleotidase (EC 3.1.3.91, 3.1.3.5) | protein | 278 | 45% helix, 21% strand | Q969T7 |
| D | 7-methylguanosine phosphate-specific 5'-nucleotidase (EC 3.1.3.91, 3.1.3.5) | protein | 277 | 46% helix, 21% strand | Q969T7 |
Ligands and binding sites
- IPQ · N7-(3,4-difluorobenzyl) guanine · ligand · 4 copies · chains A, B, C, D
- RBL · D-ribulose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 29 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.73 | 0.80 | 48 | IPQ, RBL, EDO, MG, PO4 |
| 2 | 611 | 0.73 | 0.80 | 54 | IPQ, RBL, EDO, MG, PO4 |
| 3 | 607 | 0.71 | 0.79 | 48 | IPQ, RBL, EDO, MG, PO4, SO4 |
| 4 | 580 | 0.71 | 0.79 | 47 | IPQ, RBL, EDO, MG, PO4, SO4 |
| 5 | 537 | 0.62 | 0.75 | 62 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 336 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 288 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 265 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 56 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7ZEH · Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7Guanine · the same entry in another collection · chain D against D, TM-score 1.00
- Q969T7 · AlphaFold monomer V2.0 prediction for 7-methylguanosine phosphate- specific… · a predicted model of the same protein · chain B 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 Q969T7
- Elsewhere: RCSB PDB 7ZEH · PDBe 7ZEH · UniProt Q969T7
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