6YT4

Crystal structure of the N112A mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2

Maliar, N.Kovalev, K.Baeken, C.Balandin, T.Astashkin, R.Rulev, M.Alekseev, A.Ilyinsky, N.Rogachev, A.Chupin, V.Dolgikh, D.Kirpichnikov, M.Gordeliy, V.

(2020) Crystals (Basel) 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium pumping rhodopsinA,
B,
C [auth D],
D [auth E],
E [auth C]
288Dokdonia eikastaMutation(s): 1 
Gene Names: NaR
Membrane Entity: Yes 
UniProt
Find proteins for N0DKS8 (Dokdonia eikasta)
Explore N0DKS8 
Go to UniProtKB:  N0DKS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN0DKS8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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F [auth A],
IB [auth C],
JA [auth D],
R [auth B],
VA [auth E]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
BOG
Query on BOG

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AA [auth B],
DB [auth E],
MA [auth D],
N [auth A],
OB [auth C]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
RET
Query on RET

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BA [auth B],
FB [auth E],
O [auth A],
PB [auth C],
QA [auth D]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
LFA
Query on LFA

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AB [auth E]
BB [auth E]
CA [auth B]
EB [auth E]
FA [auth D]
AB [auth E],
BB [auth E],
CA [auth B],
EB [auth E],
FA [auth D],
GA [auth D],
H [auth A],
HA [auth D],
IA [auth D],
J [auth A],
JB [auth C],
K [auth A],
KB [auth C],
LA [auth D],
LB [auth C],
MB [auth C],
NB [auth C],
OA [auth D],
PA [auth D],
S [auth B],
SA [auth E],
T [auth B],
TA [auth E],
U [auth B],
W [auth B],
X [auth B],
XA [auth E],
ZA [auth E]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
OLA
Query on OLA

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CB [auth E]
DA [auth B]
G [auth A]
HB [auth C]
I [auth A]
CB [auth E],
DA [auth B],
G [auth A],
HB [auth C],
I [auth A],
KA [auth D],
L [auth A],
M [auth A],
NA [auth D],
P [auth A],
UA [auth E],
V [auth B],
WA [auth E],
Y [auth B],
YA [auth E],
Z [auth B]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
NA (Subject of Investigation/LOI)
Query on NA

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EA [auth B],
GB [auth E],
Q [auth A],
QB [auth C],
RA [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.84α = 90
b = 239.7β = 90
c = 134.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation17-00-00164
Russian Foundation for Basic ResearchRussian Federation17-00-00165
Russian Foundation for Basic ResearchRussian Federation17-00-00167

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary