4Z9M

Crystal structure of human sarcomeric mitochondrial creatine kinase

PDB DOI: https://doi.org/10.2210/pdb4Z9M/pdb
Entry: 4Z9M supersedes: 2GL6

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

Deposited: 2015-04-10 Released: 2015-04-22
Deposition Author(s): Rabeh, W.M., Tempel, W., Nedyalkova, L., Landry, R., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Creatine kinase S-type, mitochondrial	A, B, C, D, E A, B, C, D, E, F, G, H	392	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17540
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain PB [auth G] SDF format, chain DB [auth F] SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain NA [auth E] SDF format, chain Q [auth B] SDF format, chain VB [auth H] SDF format, chain X [auth C] MOL2 format, chain PB [auth G] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain VB [auth H] MOL2 format, chain X [auth C]	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		Interactions Focus chain DB [auth F] Focus chain EA [auth D] Focus chain I [auth A] Focus chain NA [auth E] Focus chain PB [auth G] Focus chain Q [auth B] Focus chain VB [auth H] Focus chain X [auth C] Interactions & Density Focus chain DB [auth F] Focus chain EA [auth D] Focus chain I [auth A] Focus chain NA [auth E] Focus chain PB [auth G] Focus chain Q [auth B] Focus chain VB [auth H] Focus chain X [auth C]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BC [auth H] SDF format, chain CB [auth E] SDF format, chain FA [auth D] SDF format, chain UA [auth E] SDF format, chain W [auth B] SDF format, chain Y [auth C] SDF format, chain AB [auth E] SDF format, chain AC [auth H] SDF format, chain BA [auth C] SDF format, chain BB [auth E] SDF format, chain CA [auth C] SDF format, chain CC [auth H] SDF format, chain DA [auth C] SDF format, chain DC [auth H] SDF format, chain EB [auth F] SDF format, chain EC [auth H] SDF format, chain FB [auth F] SDF format, chain FC [auth H] SDF format, chain GA [auth D] SDF format, chain GB [auth F] SDF format, chain GC [auth H] SDF format, chain HA [auth D] SDF format, chain HB [auth F] SDF format, chain HC [auth H] SDF format, chain IA [auth D] SDF format, chain IB [auth F] SDF format, chain IC [auth H] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain KB [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain LB [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain MB [auth F] SDF format, chain N [auth A] SDF format, chain NB [auth F] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain OB [auth F] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain QB [auth G] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain RB [auth G] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain SB [auth G] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain TB [auth G] SDF format, chain U [auth B] SDF format, chain UB [auth G] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain WB [auth H] SDF format, chain XA [auth E] SDF format, chain XB [auth H] SDF format, chain YA [auth E] SDF format, chain YB [auth H] SDF format, chain Z [auth C] SDF format, chain ZA [auth E] SDF format, chain ZB [auth H] MOL2 format, chain AA [auth C] MOL2 format, chain BC [auth H] MOL2 format, chain CB [auth E] MOL2 format, chain FA [auth D] MOL2 format, chain UA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain AB [auth E] MOL2 format, chain AC [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain CC [auth H] MOL2 format, chain DA [auth C] MOL2 format, chain DC [auth H] MOL2 format, chain EB [auth F] MOL2 format, chain EC [auth H] MOL2 format, chain FB [auth F] MOL2 format, chain FC [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth F] MOL2 format, chain GC [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth F] MOL2 format, chain HC [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth F] MOL2 format, chain IC [auth H] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain OB [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain QB [auth G] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain RB [auth G] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth G] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth G] MOL2 format, chain U [auth B] MOL2 format, chain UB [auth G] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain WB [auth H] MOL2 format, chain XA [auth E] MOL2 format, chain XB [auth H] MOL2 format, chain YA [auth E] MOL2 format, chain YB [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth E] MOL2 format, chain ZB [auth H]	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		Interactions Focus chain AA [auth C] Focus chain AB [auth E] Focus chain AC [auth H] Focus chain BA [auth C] Focus chain BB [auth E] Focus chain BC [auth H] Focus chain CA [auth C] Focus chain CB [auth E] Focus chain CC [auth H] Focus chain DA [auth C] Focus chain DC [auth H] Focus chain EB [auth F] Focus chain EC [auth H] Focus chain FA [auth D] Focus chain FB [auth F] Focus chain FC [auth H] Focus chain GA [auth D] Focus chain GB [auth F] Focus chain GC [auth H] Focus chain HA [auth D] Focus chain HB [auth F] Focus chain HC [auth H] Focus chain IA [auth D] Focus chain IB [auth F] Focus chain IC [auth H] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain QB [auth G] Focus chain R [auth B] Focus chain RA [auth E] Focus chain RB [auth G] Focus chain S [auth B] Focus chain SA [auth E] Focus chain SB [auth G] Focus chain T [auth B] Focus chain TA [auth E] Focus chain TB [auth G] Focus chain U [auth B] Focus chain UA [auth E] Focus chain UB [auth G] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain WB [auth H] Focus chain XA [auth E] Focus chain XB [auth H] Focus chain Y [auth C] Focus chain YA [auth E] Focus chain YB [auth H] Focus chain Z [auth C] Focus chain ZA [auth E] Focus chain ZB [auth H] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth E] Focus chain AC [auth H] Focus chain BA [auth C] Focus chain BB [auth E] Focus chain BC [auth H] Focus chain CA [auth C] Focus chain CB [auth E] Focus chain CC [auth H] Focus chain DA [auth C] Focus chain DC [auth H] Focus chain EB [auth F] Focus chain EC [auth H] Focus chain FA [auth D] Focus chain FB [auth F] Focus chain FC [auth H] Focus chain GA [auth D] Focus chain GB [auth F] Focus chain GC [auth H] Focus chain HA [auth D] Focus chain HB [auth F] Focus chain HC [auth H] Focus chain IA [auth D] Focus chain IB [auth F] Focus chain IC [auth H] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain QB [auth G] Focus chain R [auth B] Focus chain RA [auth E] Focus chain RB [auth G] Focus chain S [auth B] Focus chain SA [auth E] Focus chain SB [auth G] Focus chain T [auth B] Focus chain TA [auth E] Focus chain TB [auth G] Focus chain U [auth B] Focus chain UA [auth E] Focus chain UB [auth G] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain WB [auth H] Focus chain XA [auth E] Focus chain XB [auth H] Focus chain Y [auth C] Focus chain YA [auth E] Focus chain YB [auth H] Focus chain Z [auth C] Focus chain ZA [auth E] Focus chain ZB [auth H]

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 = 93.057	α = 70.12
b = 106.058	β = 84.57
c = 114.932	γ = 68.61

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-04-22

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 2GL6

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