Research workbench
Crystal structure of human purine nucleoside phosphorylase in complex with dadme-immg
Analyse Crystal structure of human purine nucleoside phosphorylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PHB
- Type
- protein
- Length
- 1,718 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- P00491
- Ligands
- IM5, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 288 | 32% helix, 23% strand | P00491 |
| Q | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 287 | 32% helix, 23% strand | P00491 |
| S | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 286 | 34% helix, 23% strand | P00491 |
| T | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 287 | 32% helix, 23% strand | P00491 |
| U | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 285 | 32% helix, 23% strand | P00491 |
| Y | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 285 | 32% helix, 23% strand | P00491 |
Ligands and binding sites
- IM5 · 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one · ligand · 6 copies · chains E, Y, Q, S, U, T
- PO4 · Phosphate ion · ion · 12 copies · chains E, Q, Y, S, U, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.80 | 0.97 | 29 | IM5, PO4 |
| 2 | 129 | 0.80 | 0.98 | 31 | IM5, PO4 |
| 3 | 135 | 0.80 | 0.97 | 33 | IM5, PO4 |
| 4 | 128 | 0.80 | 0.98 | 31 | IM5, PO4 |
| 5 | 105 | 0.80 | 0.98 | 17 | empty |
Interfaces
7 interfaces between chains.
- T–U · 1471 Ų buried · 19 hydrogen bonds · protein-protein
- E–Q · 1458 Ų buried · 18 hydrogen bonds · protein-protein
- Q–Y · 1438 Ų buried · 17 hydrogen bonds · protein-protein
- S–T · 1367 Ų buried · 19 hydrogen bonds · protein-protein
- E–Y · 1355 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3PHB · Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG · the same entry in another collection · chain Y against Y, TM-score 1.00
- P00491 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P00491) · a predicted model of the same protein · chain U 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 P00491
- Elsewhere: RCSB PDB 3PHB · PDBe 3PHB · UniProt P00491
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