Download MendeleyPhosphoglycerate mutase 1 complexed with a small molecule inhibitor KH2
Jiang, L.L., Zhou, L.To be published.
5Y65
Phosphoglycerate mutase 1 complexed with a small molecule inhibitor KH2
- PDB DOI: https://doi.org/10.2210/pdb5Y65/pdb
- Classification: ISOMERASE/INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2017-08-10 Released: 2018-12-05
- Funding Organization(s): National Science Foundation (China)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.248
- R-Value Work: 0.198
- R-Value Observed: 0.200
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 mutase 1 | A [auth B] | 262 | Homo sapiens | Mutation(s): 0 Gene Names: PGAM1, PGAMA, CDABP0006 EC: 5.4.2.11 (PDB Primary Data), 5.4.2.4 (PDB Primary Data) |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P18669 (Homo sapiens) Explore P18669 Go to UniProtKB: P18669 | |||||
PHAROS: P18669 GTEx: ENSG00000171314 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P18669 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Phosphoglycerate mutase 1 | B [auth C] | 262 | Homo sapiens | Mutation(s): 0 Gene Names: PGAM1, PGAMA, CDABP0006 EC: 5.4.2.11 (PDB Primary Data), 5.4.2.4 (PDB Primary Data) |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P18669 (Homo sapiens) Explore P18669 Go to UniProtKB: P18669 | |||||
PHAROS: P18669 GTEx: ENSG00000171314 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P18669 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HKB Query on HKB | E [auth C] | ~{N}-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]-4-(dimethylamino)benzenesulfonamide C22 H18 N2 O6 S CJPMCWRDXYBEBQ-UHFFFAOYSA-N |  | ||
| MES Query on MES | D [auth C] | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N |  | ||
| CL Query on CL | C [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| NEP Query on NEP | B [auth C] | L-PEPTIDE LINKING | C6 H10 N3 O5 P |  | HIS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.248
- R-Value Work: 0.198
- R-Value Observed: 0.200
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 79.193 | α = 90 |
| b = 82.929 | β = 90 |
| c = 99.797 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| HKL-2000 | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-12-05 Deposition Author(s): Jiang, L.L., Zhou, L.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Science Foundation (China) | China | 21472026 |
Revision History (Full details and data files)
- Version 1.0: 2018-12-05
Type: Initial release
