4Z9M

Crystal structure of human sarcomeric mitochondrial creatine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of human sarcomeric mitochondrial creatine kinase

Rabeh, W.M.Tempel, W.Nedyalkova, L.Landry, R.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Bochkarev, A.Park, H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Creatine kinase S-type, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G, H
392Homo sapiensMutation(s): 0 
Gene Names: CKMT2
EC: 2.7.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P17540 (Homo sapiens)
Explore P17540 
Go to UniProtKB:  P17540
PHAROS:  P17540
GTEx:  ENSG00000131730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17540
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
DB [auth F]
EA [auth D]
I [auth A]
NA [auth E]
PB [auth G]
DB [auth F],
EA [auth D],
I [auth A],
NA [auth E],
PB [auth G],
Q [auth B],
VB [auth H],
X [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth E]
AC [auth H]
BA [auth C]
BB [auth E]
AA [auth C],
AB [auth E],
AC [auth H],
BA [auth C],
BB [auth E],
BC [auth H],
CA [auth C],
CB [auth E],
CC [auth H],
DA [auth C],
DC [auth H],
EB [auth F],
EC [auth H],
FA [auth D],
FB [auth F],
FC [auth H],
GA [auth D],
GB [auth F],
GC [auth H],
HA [auth D],
HB [auth F],
HC [auth H],
IA [auth D],
IB [auth F],
IC [auth H],
J [auth A],
JA [auth D],
JB [auth F],
K [auth A],
KA [auth D],
KB [auth F],
L [auth A],
LA [auth D],
LB [auth F],
M [auth A],
MA [auth D],
MB [auth F],
N [auth A],
NB [auth F],
O [auth A],
OA [auth E],
OB [auth F],
P [auth A],
PA [auth E],
QA [auth E],
QB [auth G],
R [auth B],
RA [auth E],
RB [auth G],
S [auth B],
SA [auth E],
SB [auth G],
T [auth B],
TA [auth E],
TB [auth G],
U [auth B],
UA [auth E],
UB [auth G],
V [auth B],
VA [auth E],
W [auth B],
WA [auth E],
WB [auth H],
XA [auth E],
XB [auth H],
Y [auth C],
YA [auth E],
YB [auth H],
Z [auth C],
ZA [auth E],
ZB [auth H]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.057α = 70.12
b = 106.058β = 84.57
c = 114.932γ = 68.61
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description