3GR4
Activator-Bound Structure of Human Pyruvate Kinase M2
- PDB DOI: https://doi.org/10.2210/pdb3GR4/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2009-03-24 Released: 2009-04-07 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.231 
- R-Value Work: 0.208 
- R-Value Observed: 0.208 
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Pyruvate kinase isozymes M1/M2 | 550 | Homo sapiens | Mutation(s): 0  Gene Names: PKM2, PK2, PK3, PKM EC: 2.7.1.40 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P14618 (Homo sapiens) Explore P14618  Go to UniProtKB:  P14618 | |||||
PHAROS:  P14618 GTEx:  ENSG00000067225  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P14618 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
DYY Query on DYY | CA [auth D], G [auth A] | 1-[(2,6-difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine C18 H18 F2 N2 O6 S2 SHWNKRPMUBFWKE-UHFFFAOYSA-N | |||
ADP Query on ADP | N [auth A] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N | |||
FBP Query on FBP | DA [auth D], E [auth A], O [auth B], X [auth C] | 1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N | |||
TLA Query on TLA | BA [auth C] EA [auth D] F [auth A] JA [auth D] P [auth B] | L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N | |||
UNX Query on UNX | AA [auth C] FA [auth D] GA [auth D] H [auth A] HA [auth D] | UNKNOWN ATOM OR ION X |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.231 
- R-Value Work: 0.208 
- R-Value Observed: 0.208 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 81.275 | α = 90 |
b = 153.206 | β = 102.91 |
c = 93.138 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Coot | model building |
MolProbity | model building |
prodrg | refinement |
Entry History 
Deposition Data
- Released Date: 2009-04-07  Deposition Author(s): Hong, B., Dimov, S., Tempel, W., Auld, D., Thomas, C., Boxer, M., Jianq, J.-K., Skoumbourdis, A., Min, S., Southall, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Inglese, J., Park, H., Structural Genomics Consortium (SGC)
Revision History (Full details and data files)
- Version 1.0: 2009-04-07
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.4: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary