5X0I
Crystal structure of PKM2 R399E mutant complexed with FBP and serine
- PDB DOI: https://doi.org/10.2210/pdb5X0I/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2017-01-20 Released: 2018-01-31 
- Funding Organization(s): NHRI
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.64 Å
- R-Value Free: 0.218 
- R-Value Work: 0.180 
- R-Value Observed: 0.182 
This is version 2.1 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 PKM | 551 | Homo sapiens | Mutation(s): 1  Gene Names: PKM, OIP3, PK2, PK3, PKM2 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 | |
FBP Query on FBP | E [auth A], J [auth B], O [auth C], T [auth D] | 1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N | |||
SER Query on SER | F [auth A], K [auth B], P [auth C], U [auth D] | SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N | |||
PYR Query on PYR | G [auth A], L [auth B], Q [auth C], V [auth D] | PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N | |||
K Query on K | I [auth A], N [auth B], S [auth C], X [auth D] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
MG Query on MG | H [auth A], M [auth B], R [auth C], W [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.64 Å
- R-Value Free: 0.218 
- R-Value Work: 0.180 
- R-Value Observed: 0.182 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 116.601 | α = 90 |
b = 137.875 | β = 90 |
c = 149.709 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-01-31  Deposition Author(s): Wang, W.C., Chen, T.J.
Funding Organization | Location | Grant Number |
---|---|---|
NHRI | Taiwan | NHRI-EX105-10517BI |
Revision History (Full details and data files)
- Version 1.0: 2018-01-31
Type: Initial release - Version 1.1: 2019-04-03
Changes: Data collection, Database references - Version 1.2: 2019-11-20
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-11-22
Changes: Refinement description