Download MendeleyCrystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)
Saijo, S., Nishino, A., Kishishita, S., Shirouzu, M., Yokoyama, S.To be published.
2Z0B
Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)
- DOI: 10.2210/pdb2Z0B/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2007-05-07 Released: 2008-05-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.243
- R-Value Work: 0.221
- R-Value Observed: 0.222
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Putative glycerophosphodiester phosphodiesterase 5 | A, B, C, D, E, F | 131 | Homo sapiens | Mutation(s): 0 Gene Names: GDE5, KIAA1434, GPCPD1 EC: 3.1 (PDB Primary Data), 3.1.4.2 (UniProt) |  |
Find proteins for Q9NPB8 (Homo sapiens) Explore Q9NPB8 Go to UniProtKB: Q9NPB8 | |||||
NIH Common Fund Data Resources | |||||
PHAROS: Q9NPB8 GTEx: ENSG00000125772 | |||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | A, F | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A,B,C,D,E,F | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.243
- R-Value Work: 0.221
- R-Value Observed: 0.222
- Space Group: P 31
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 111.04 | α = 90 |
| b = 111.04 | β = 90 |
| c = 77.385 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| BSS | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SOLVE | phasing |
Entry History
Deposition Data
- Deposited Date: 2007-05-07
- Released Date: 2008-05-06 Deposition Author(s): Saijo, S., Nishino, A., Kishishita, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
