6BG2 | pdb_00006bg2

Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain in AMP-PNP bound state

PDB DOI: https://doi.org/10.2210/pdb6BG2/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2017-10-27 Released: 2018-10-31
Deposition Author(s): Qin, L., Sankaran, B., Kim, C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.215 (Depositor), 0.216 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain

Qin, L., Sankaran, B., Casteel, D., Kim, C.

To be published.

Macromolecule Content

Total Structure Weight: 160.36 kDa
Atom Count: 11,857
Modeled Residue Count: 1,325
Deposited Residue Count: 1,388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent protein kinase 1	A [auth C], B, C [auth A], D	347	Homo sapiens	Mutation(s): 0 Gene Names: PRKG1, PRKG1B, PRKGR1A, PRKGR1B EC: 2.7.11.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q13976 (Homo sapiens) Explore Q13976 Go to UniProtKB: Q13976
PHAROS: Q13976 GTEx: ENSG00000185532
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13976
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth A] SDF format, chain N [auth D] SDF format, chain E [auth C] MOL2 format, chain H [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth D] MOL2 format, chain E [auth C] mmCIF format, chain H [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth D] mmCIF format, chain E [auth C]	E [auth C], H [auth B], K [auth A], N [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain E [auth C] Focus chain H [auth B] Focus chain K [auth A] Focus chain N [auth D] Interactions & Density Focus chain E [auth C] Focus chain H [auth B] Focus chain K [auth A] Focus chain N [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth A] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain M [auth A] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth A] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain M [auth A] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth A] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain M [auth A]	F [auth C] G [auth C] I [auth B] J [auth B] L [auth A] F [auth C], G [auth C], I [auth B], J [auth B], L [auth A], M [auth A], O [auth D], P [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth C] Focus chain G [auth C] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth D] Focus chain P [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A [auth C], B, C [auth A], D	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.215 (Depositor), 0.216 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.39	α = 90
b = 98.5	β = 133.47
c = 116.424	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-31

Deposition Author(s):

Qin, L.

Sankaran, B.

Kim, C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM090161-08

Revision History (Full details and data files)

Version 1.0: 2018-10-31
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary

6BG2 | pdb_00006bg2

Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain in AMP-PNP bound state

Literature

Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand