4Z9M | pdb_00004z9m

Crystal structure of human sarcomeric mitochondrial creatine kinase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.236 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.202 (Depositor) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4Z9M

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.

Macromolecule Content 

  • Total Structure Weight: 360.91 kDa 
  • Atom Count: 23,253 
  • Modeled Residue Count: 2,818 
  • Deposited Residue Count: 3,136 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  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 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.202 (Depositor) 
  • R-Value Observed: 0.203 (Depositor) 
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 


View more in-depth experimental data

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