6FIZ | pdb_00006fiz

Crystal Structure of CNG mimicking NaK-EAPP mutant (T67A) cocrystallized with K+

PDB DOI: https://doi.org/10.2210/pdb6FIZ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bacillus cereus ATCC 14579, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2018-01-19 Released: 2019-03-06
Deposition Author(s): Napolitano, L.M.R., De March, M., Steiner, R.A., Onesti, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free:
0.269 (Depositor), 0.275 (DCC)
R-Value Work:
0.235 (Depositor), 0.240 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of CNG mimicking NaK-EAPP mutant (T67A) cocrystallized with K+

Napolitano, L.M.R., De March, M., Onesti, S., Steiner, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 170.51 kDa
Atom Count: 11,844
Modeled Residue Count: 1,462
Deposited Residue Count: 1,504
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	94	Bacillus cereus ATCC 14579, Homo sapiens	Mutation(s): 1 Gene Names: BC_0669, CNGA2, CNCA, CNCA1, CNCG2 Membrane Entity: Yes
UniProt
Find proteins for Q81HW2 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81HW2 Go to UniProtKB: Q81HW2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q81HW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain JC [auth N] SDF format, chain KB [auth J] SDF format, chain NA [auth F] SDF format, chain QA [auth G] SDF format, chain LB [auth J] SDF format, chain AC [auth M] MOL2 format, chain DA [auth D] MOL2 format, chain JC [auth N] MOL2 format, chain KB [auth J] MOL2 format, chain NA [auth F] MOL2 format, chain QA [auth G] MOL2 format, chain LB [auth J] MOL2 format, chain AC [auth M] mmCIF format, chain DA [auth D] mmCIF format, chain JC [auth N] mmCIF format, chain KB [auth J] mmCIF format, chain NA [auth F] mmCIF format, chain QA [auth G] mmCIF format, chain LB [auth J] mmCIF format, chain AC [auth M]	AC [auth M] DA [auth D] JC [auth N] KB [auth J] LB [auth J] AC [auth M], DA [auth D], JC [auth N], KB [auth J], LB [auth J], NA [auth F], QA [auth G]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AC [auth M] Focus chain DA [auth D] Focus chain JC [auth N] Focus chain KB [auth J] Focus chain LB [auth J] Focus chain NA [auth F] Focus chain QA [auth G] Interactions & Density Focus chain AC [auth M] Focus chain DA [auth D] Focus chain JC [auth N] Focus chain KB [auth J] Focus chain LB [auth J] Focus chain NA [auth F] Focus chain QA [auth G]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain BB [auth J] SDF format, chain DB [auth J] SDF format, chain EA [auth E] SDF format, chain EB [auth J] SDF format, chain FB [auth J] SDF format, chain FC [auth N] SDF format, chain HA [auth E] SDF format, chain HB [auth J] SDF format, chain JB [auth J] SDF format, chain KC [auth O] SDF format, chain LA [auth F] SDF format, chain MB [auth K] SDF format, chain NC [auth O] SDF format, chain OA [auth G] SDF format, chain Q [auth A] SDF format, chain QB [auth L] SDF format, chain QC [auth P] SDF format, chain RB [auth M] SDF format, chain SA [auth H] SDF format, chain SB [auth M] SDF format, chain UB [auth M] SDF format, chain W [auth B] SDF format, chain WA [auth I] SDF format, chain XA [auth I] SDF format, chain Y [auth C] SDF format, chain Z [auth D] SDF format, chain X [auth B] SDF format, chain WB [auth M] SDF format, chain VB [auth M] SDF format, chain VA [auth I] SDF format, chain V [auth B] SDF format, chain UA [auth H] SDF format, chain TB [auth M] SDF format, chain TA [auth H] SDF format, chain RA [auth H] SDF format, chain R [auth A] SDF format, chain PC [auth P] SDF format, chain PB [auth L] SDF format, chain PA [auth G] SDF format, chain OC [auth P] SDF format, chain OB [auth K] SDF format, chain NB [auth K] SDF format, chain MC [auth O] SDF format, chain MA [auth F] SDF format, chain LC [auth O] SDF format, chain IC [auth N] SDF format, chain IB [auth J] SDF format, chain HC [auth N] SDF format, chain GC [auth N] SDF format, chain GB [auth J] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain EC [auth N] SDF format, chain DC [auth N] SDF format, chain CC [auth N] SDF format, chain CB [auth J] SDF format, chain CA [auth D] SDF format, chain BC [auth N] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth J] MOL2 format, chain DB [auth J] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth J] MOL2 format, chain FB [auth J] MOL2 format, chain FC [auth N] MOL2 format, chain HA [auth E] MOL2 format, chain HB [auth J] MOL2 format, chain JB [auth J] MOL2 format, chain KC [auth O] MOL2 format, chain LA [auth F] MOL2 format, chain MB [auth K] MOL2 format, chain NC [auth O] MOL2 format, chain OA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth L] MOL2 format, chain QC [auth P] MOL2 format, chain RB [auth M] MOL2 format, chain SA [auth H] MOL2 format, chain SB [auth M] MOL2 format, chain UB [auth M] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth I] MOL2 format, chain XA [auth I] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth B] MOL2 format, chain WB [auth M] MOL2 format, chain VB [auth M] MOL2 format, chain VA [auth I] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain TB [auth M] MOL2 format, chain TA [auth H] MOL2 format, chain RA [auth H] MOL2 format, chain R [auth A] MOL2 format, chain PC [auth P] MOL2 format, chain PB [auth L] MOL2 format, chain PA [auth G] MOL2 format, chain OC [auth P] MOL2 format, chain OB [auth K] MOL2 format, chain NB [auth K] MOL2 format, chain MC [auth O] MOL2 format, chain MA [auth F] MOL2 format, chain LC [auth O] MOL2 format, chain IC [auth N] MOL2 format, chain IB [auth J] MOL2 format, chain HC [auth N] MOL2 format, chain GC [auth N] MOL2 format, chain GB [auth J] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain EC [auth N] MOL2 format, chain DC [auth N] MOL2 format, chain CC [auth N] MOL2 format, chain CB [auth J] MOL2 format, chain CA [auth D] MOL2 format, chain BC [auth N] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth J] mmCIF format, chain DB [auth J] mmCIF format, chain EA [auth E] mmCIF format, chain EB [auth J] mmCIF format, chain FB [auth J] mmCIF format, chain FC [auth N] mmCIF format, chain HA [auth E] mmCIF format, chain HB [auth J] mmCIF format, chain JB [auth J] mmCIF format, chain KC [auth O] mmCIF format, chain LA [auth F] mmCIF format, chain MB [auth K] mmCIF format, chain NC [auth O] mmCIF format, chain OA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth L] mmCIF format, chain QC [auth P] mmCIF format, chain RB [auth M] mmCIF format, chain SA [auth H] mmCIF format, chain SB [auth M] mmCIF format, chain UB [auth M] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth I] mmCIF format, chain XA [auth I] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth B] mmCIF format, chain WB [auth M] mmCIF format, chain VB [auth M] mmCIF format, chain VA [auth I] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain TB [auth M] mmCIF format, chain TA [auth H] mmCIF format, chain RA [auth H] mmCIF format, chain R [auth A] mmCIF format, chain PC [auth P] mmCIF format, chain PB [auth L] mmCIF format, chain PA [auth G] mmCIF format, chain OC [auth P] mmCIF format, chain OB [auth K] mmCIF format, chain NB [auth K] mmCIF format, chain MC [auth O] mmCIF format, chain MA [auth F] mmCIF format, chain LC [auth O] mmCIF format, chain IC [auth N] mmCIF format, chain IB [auth J] mmCIF format, chain HC [auth N] mmCIF format, chain GC [auth N] mmCIF format, chain GB [auth J] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain EC [auth N] mmCIF format, chain DC [auth N] mmCIF format, chain CC [auth N] mmCIF format, chain CB [auth J] mmCIF format, chain CA [auth D] mmCIF format, chain BC [auth N]	AA [auth D] BA [auth D] BB [auth J] BC [auth N] CA [auth D] AA [auth D], BA [auth D], BB [auth J], BC [auth N], CA [auth D], CB [auth J], CC [auth N], DB [auth J], DC [auth N], EA [auth E], EB [auth J], EC [auth N], FA [auth E], FB [auth J], FC [auth N], GA [auth E], GB [auth J], GC [auth N], HA [auth E], HB [auth J], HC [auth N], IB [auth J], IC [auth N], JB [auth J], KC [auth O], LA [auth F], LC [auth O], MA [auth F], MB [auth K], MC [auth O], NB [auth K], NC [auth O], OA [auth G], OB [auth K], OC [auth P], PA [auth G], PB [auth L], PC [auth P], Q [auth A], QB [auth L], QC [auth P], R [auth A], RA [auth H], RB [auth M], SA [auth H], SB [auth M], TA [auth H], TB [auth M], UA [auth H], UB [auth M], V [auth B], VA [auth I], VB [auth M], W [auth B], WA [auth I], WB [auth M], X [auth B], XA [auth I], Y [auth C], Z [auth D]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain BB [auth J] Focus chain BC [auth N] Focus chain CA [auth D] Focus chain CB [auth J] Focus chain CC [auth N] Focus chain DB [auth J] Focus chain DC [auth N] Focus chain EA [auth E] Focus chain EB [auth J] Focus chain EC [auth N] Focus chain FA [auth E] Focus chain FB [auth J] Focus chain FC [auth N] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain GC [auth N] Focus chain HA [auth E] Focus chain HB [auth J] Focus chain HC [auth N] Focus chain IB [auth J] Focus chain IC [auth N] Focus chain JB [auth J] Focus chain KC [auth O] Focus chain LA [auth F] Focus chain LC [auth O] Focus chain MA [auth F] Focus chain MB [auth K] Focus chain MC [auth O] Focus chain NB [auth K] Focus chain NC [auth O] Focus chain OA [auth G] Focus chain OB [auth K] Focus chain OC [auth P] Focus chain PA [auth G] Focus chain PB [auth L] Focus chain PC [auth P] Focus chain Q [auth A] Focus chain QB [auth L] Focus chain QC [auth P] Focus chain R [auth A] Focus chain RA [auth H] Focus chain RB [auth M] Focus chain SA [auth H] Focus chain SB [auth M] Focus chain TA [auth H] Focus chain TB [auth M] Focus chain UA [auth H] Focus chain UB [auth M] Focus chain V [auth B] Focus chain VA [auth I] Focus chain VB [auth M] Focus chain W [auth B] Focus chain WA [auth I] Focus chain WB [auth M] Focus chain X [auth B] Focus chain XA [auth I] Focus chain Y [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain BB [auth J] Focus chain BC [auth N] Focus chain CA [auth D] Focus chain CB [auth J] Focus chain CC [auth N] Focus chain DB [auth J] Focus chain DC [auth N] Focus chain EA [auth E] Focus chain EB [auth J] Focus chain EC [auth N] Focus chain FA [auth E] Focus chain FB [auth J] Focus chain FC [auth N] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain GC [auth N] Focus chain HA [auth E] Focus chain HB [auth J] Focus chain HC [auth N] Focus chain IB [auth J] Focus chain IC [auth N] Focus chain JB [auth J] Focus chain KC [auth O] Focus chain LA [auth F] Focus chain LC [auth O] Focus chain MA [auth F] Focus chain MB [auth K] Focus chain MC [auth O] Focus chain NB [auth K] Focus chain NC [auth O] Focus chain OA [auth G] Focus chain OB [auth K] Focus chain OC [auth P] Focus chain PA [auth G] Focus chain PB [auth L] Focus chain PC [auth P] Focus chain Q [auth A] Focus chain QB [auth L] Focus chain QC [auth P] Focus chain R [auth A] Focus chain RA [auth H] Focus chain RB [auth M] Focus chain SA [auth H] Focus chain SB [auth M] Focus chain TA [auth H] Focus chain TB [auth M] Focus chain UA [auth H] Focus chain UB [auth M] Focus chain V [auth B] Focus chain VA [auth I] Focus chain VB [auth M] Focus chain W [auth B] Focus chain WA [auth I] Focus chain WB [auth M] Focus chain X [auth B] Focus chain XA [auth I] Focus chain Y [auth C] Focus chain Z [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain IA [auth E] SDF format, chain KA [auth E] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain XB [auth M] SDF format, chain YA [auth I] SDF format, chain ZB [auth M] SDF format, chain ZA [auth I] SDF format, chain YB [auth M] SDF format, chain S [auth A] SDF format, chain JA [auth E] MOL2 format, chain AB [auth I] MOL2 format, chain IA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain XB [auth M] MOL2 format, chain YA [auth I] MOL2 format, chain ZB [auth M] MOL2 format, chain ZA [auth I] MOL2 format, chain YB [auth M] MOL2 format, chain S [auth A] MOL2 format, chain JA [auth E] mmCIF format, chain AB [auth I] mmCIF format, chain IA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain XB [auth M] mmCIF format, chain YA [auth I] mmCIF format, chain ZB [auth M] mmCIF format, chain ZA [auth I] mmCIF format, chain YB [auth M] mmCIF format, chain S [auth A] mmCIF format, chain JA [auth E]	AB [auth I] IA [auth E] JA [auth E] KA [auth E] S [auth A] AB [auth I], IA [auth E], JA [auth E], KA [auth E], S [auth A], T [auth A], U [auth A], XB [auth M], YA [auth I], YB [auth M], ZA [auth I], ZB [auth M]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain XB [auth M] Focus chain YA [auth I] Focus chain YB [auth M] Focus chain ZA [auth I] Focus chain ZB [auth M] Interactions & Density Focus chain AB [auth I] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain XB [auth M] Focus chain YA [auth I] Focus chain YB [auth M] Focus chain ZA [auth I] Focus chain ZB [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.269 (Depositor), 0.275 (DCC)
R-Value Work: 0.235 (Depositor), 0.240 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.22	α = 90
b = 135.25	β = 91.95
c = 67.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-03-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-03-06
Type: Initial release
Version 1.1: 2019-04-03
Changes: Data collection
Version 1.2: 2019-06-26
Changes: Data collection, Database references, Source and taxonomy, Structure summary
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description