Download MendeleyHuman isocitrate dehydrogenase 1 bound with isocitrate
Nordlund, P., Chen, D., Jansson, A., Larsson, A.To be published.
5YFN
Human isocitrate dehydrogenase 1 bound with isocitrate
- PDB DOI: https://doi.org/10.2210/pdb5YFN/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2017-09-21 Released: 2017-10-25
- Funding Organization(s): Nanyang Technological University
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 ?
- R-Value Free: 0.226
- R-Value Work: 0.173
- R-Value Observed: 0.176
Starting Model: experimental
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This is version 1.1 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 |
| Isocitrate dehydrogenase [NADP] cytoplasmic | 421 | Homo sapiens | Mutation(s): 0 Gene Names: IDH1, PICD EC: 1.1.1.42 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O75874 (Homo sapiens) Explore O75874 Go to UniProtKB: O75874 | |||||
PHAROS: O75874 GTEx: ENSG00000138413 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O75874 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ICT Query on ICT | D [auth A], G [auth A] | ISOCITRIC ACID C6 H8 O7 ODBLHEXUDAPZAU-ZAFYKAAXSA-N |  | ||
| K Query on K | F [auth A], H [auth B] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | ||
| MG Query on MG | C [auth A], E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 ?
- R-Value Free: 0.226
- R-Value Work: 0.173
- R-Value Observed: 0.176
- Space Group: I 1 2 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 111.56 | ¦Á = 90 |
| b = 92 | ¦Â = 109.94 |
| c = 138.835 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-10-25 Deposition Author(s): Nordlund, P., Chen, D., Jansson, A., Larsson, A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Nanyang Technological University | Singapore | M060080004 |
Revision History (Full details and data files)
- Version 1.0: 2017-10-25
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
