Download MendeleyThe role of magnesium in catalysis by phosphoglycerate kinase
Cliff, M.J., Serimbetov, Z., Bisson, C., Baxter, N.J., Blackburn, G.M., Hay, S., Bowler, M.W., Waltho, J.P.To be published.
9FDN | pdb_00009fdn
Human phosphoglycerate kinase in complex with ATP and 3PG formed by cross-soaking a TSA crystal
- PDB DOI: https://doi.org/10.2210/pdb9FDN/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-05-17 Released: 2025-05-28
- Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 ?
- R-Value Free: 0.204 (Depositor), 0.176 (DCC)
- R-Value Work: 0.178 (Depositor), 0.183 (DCC)
- R-Value Observed: 0.179 (Depositor)
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Phosphoglycerate kinase 1 | 417 | Homo sapiens | Mutation(s): 0 Gene Names: PGK1, PGKA, MIG10, OK/SW-cl.110 EC: 2.7.2.3 (PDB Primary Data), 2.7.11.1 (UniProt) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00558 (Homo sapiens) Explore P00558 Go to UniProtKB: P00558 | |||||
PHAROS: P00558 GTEx: ENSG00000102144 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00558 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP (Subject of Investigation/LOI) Query on ATP | C [auth A] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
| PG4 Query on PG4 | E [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| 3PG (Subject of Investigation/LOI) Query on 3PG | D [auth A] | 3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N |  | ||
| NA Query on NA | B [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 ?
- R-Value Free: 0.204 (Depositor), 0.176 (DCC)
- R-Value Work: 0.178 (Depositor), 0.183 (DCC)
- R-Value Observed: 0.179 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 39.04 | α = 90 |
| b = 91.1 | β = 90 |
| c = 108.2 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| xia2 | data scaling |
| DIALS | data reduction |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-05-28 Deposition Author(s): Cliff, M.J., Waltho, J.P., Bowler, M.W., Baxter, N.J., Bisson, C., Blackburn, G.M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Biotechnology and Biological Sciences Research Council (BBSRC) | United Kingdom | BB/M021637/1 |
Revision History (Full details and data files)
- Version 1.0: 2025-05-28
Type: Initial release
