2Z0B | pdb_00002z0b

Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)

PDB DOI: https://doi.org/10.2210/pdb2Z0B/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2007-05-07 Released: 2008-05-06
Deposition Author(s): Saijo, S., Nishino, A., Kishishita, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.243 (Depositor), 0.217 (DCC)
R-Value Work:
0.221 (Depositor), 0.216 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2Z0B

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)

Saijo, S., Nishino, A., Kishishita, S., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 84.57 kDa
Atom Count: 5,625
Modeled Residue Count: 663
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glycerophosphodiester phosphodiesterase 5	A, B, C, D, E A, B, C, D, E, F	131	Homo sapiens	Mutation(s): 0 Gene Names: GDE5, KIAA1434 EC: 3.1 (PDB Primary Data), 3.1.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPB8 (Homo sapiens) Explore Q9NPB8 Go to UniProtKB: Q9NPB8
PHAROS: Q9NPB8 GTEx: ENSG00000125772
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NPB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth F] SDF format, chain G [auth A] MOL2 format, chain H [auth F] MOL2 format, chain G [auth A] mmCIF format, chain H [auth F] mmCIF format, chain G [auth A]	G [auth A], H [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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 (Depositor), 0.217 (DCC)
R-Value Work: 0.221 (Depositor), 0.216 (DCC)
R-Value Observed: 0.222 (Depositor)

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 Package:

Software Name	Purpose
REFMAC	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-05-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.