2UZP | pdb_00002uzp

Crystal structure of the C2 domain of human protein kinase C gamma.

PDB DOI: https://doi.org/10.2210/pdb2UZP/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-04-30 Released: 2007-05-29
Deposition Author(s): Pike, A.C.W., Amos, A., Johansson, C., Sobott, F., Savitsky, P., Berridge, G., Fedorov, O., Umeano, C., Gorrec, F., Bunkoczi, G., Debreczeni, J., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.205 (Depositor), 0.269 (DCC)
R-Value Work:
0.171 (Depositor)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of C2 Domain of Protein Kinase C Gamma

Pike, A.C.W., Amos, A., Johansson, C., Sobott, F., Savitsky, P., Berridge, G., Fedorov, O., Umeano, C., Gorrec, F., Bunkoczi, G., Debreczeni, J., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 53.3 kDa
Atom Count: 4,078
Modeled Residue Count: 426
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN KINASE C GAMMA TYPE	A, B, C	144	Homo sapiens	Mutation(s): 0 EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for P05129 (Homo sapiens) Explore P05129 Go to UniProtKB: P05129
PHAROS: P05129 GTEx: ENSG00000126583
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05129
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain EA [auth C] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain Q [auth B]	D [auth A], EA [auth C], Q [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain EA [auth C] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain EA [auth C] Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] I [auth A] J [auth A] JA [auth C] AA [auth B], BA [auth B], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], OA [auth C], PA [auth C], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C]	CA [auth B] DA [auth B] O [auth A] P [auth A] QA [auth C] CA [auth B], DA [auth B], O [auth A], P [auth A], QA [auth C], RA [auth C], SA [auth C], TA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain FA [auth C] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain R [auth B]	E [auth A], FA [auth C], R [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth C] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain FA [auth C] Focus chain R [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	F [auth A] G [auth A] GA [auth C] H [auth A] HA [auth C] F [auth A], G [auth A], GA [auth C], H [auth A], HA [auth C], IA [auth C], S [auth B], T [auth B], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.205 (Depositor), 0.269 (DCC)
R-Value Work: 0.171 (Depositor)
R-Value Observed: 0.172 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.503	α = 90
b = 138.503	β = 90
c = 68.358	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-05-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2014-03-19
Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description