MolNFT v1 · #55952 · protein
Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)
2Z0B: “Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.75). MolNFT v1 #55952 on GenesisL1: 3D structure, binding…
- PDB
- 2Z0B
- Type
- protein
- Length
- 663 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycerophosphodiester phosphodiesterase 5
- EC
- 3.1.-.-
- UniProt
- Q9NPB8
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glycerophosphodiester phosphodiesterase 5 (EC 3.1.-.-) | protein | 111 | 5% helix, 50% strand | Q9NPB8 |
| B | Putative glycerophosphodiester phosphodiesterase 5 (EC 3.1.-.-) | protein | 107 | 6% helix, 53% strand | Q9NPB8 |
| C | Putative glycerophosphodiester phosphodiesterase 5 (EC 3.1.-.-) | protein | 116 | 5% helix, 50% strand | Q9NPB8 |
| D | Putative glycerophosphodiester phosphodiesterase 5 (EC 3.1.-.-) | protein | 116 | 5% helix, 50% strand | Q9NPB8 |
| E | Putative glycerophosphodiester phosphodiesterase 5 (EC 3.1.-.-) | protein | 106 | 3% helix, 52% strand | Q9NPB8 |
| F | Putative glycerophosphodiester phosphodiesterase 5 (EC 3.1.-.-) | protein | 107 | 6% helix, 51% strand | Q9NPB8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.75 | 0.77 | 102 | PO4 |
| 2 | 1193 | 0.74 | 0.77 | 91 | PO4 |
| 3 | 128 | 0.40 | 0.75 | 24 | empty |
Interfaces
10 interfaces between chains.
- B–C · 722 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 685 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 375 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 373 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 336 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2Z0B · Crystal structure of CBM20 domain of human putative glycerophosphodiester… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9NPB8 · AlphaFold monomer V2.0 prediction for glycerophosphocholine phosphodiesterase GPCPD1… · a predicted model of the same protein · chain E against A, TM-score 0.95
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 Q9NPB8
- Elsewhere: RCSB PDB 2Z0B · PDBe 2Z0B · UniProt Q9NPB8
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