Download MendeleyCrystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate
Dong, J., Wang, S., York, J.D.To be published.
4XPD
Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate
- PDB DOI: https://doi.org/10.2210/pdb4XPD/pdb
- Classification: TRANSFERASE
- Organism(s): Saccharomyces cerevisiae, Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-01-16 Released: 2016-07-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.81 ?
- R-Value Free: 0.297
- R-Value Work: 0.236
- R-Value Observed: 0.239
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 |
| N-terminal acetyltransferase A complex subunit NAT1 | 854 | Saccharomyces cerevisiae | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P12945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12945 Go to UniProtKB: P12945 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P12945 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| N-terminal acetyltransferase A complex catalytic subunit ARD1 | 238 | Saccharomyces cerevisiae | Mutation(s): 0 EC: 2.3.1.88 (PDB Primary Data), 2.3.1.255 (UniProt) |  | |
UniProt | |||||
Find proteins for P07347 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07347 Go to UniProtKB: P07347 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07347 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| N-terminal acetyltransferase A complex subunit NAT5 | 176 | Saccharomyces cerevisiae | Mutation(s): 0 EC: 2.3.1 (PDB Primary Data), 2.3.1.258 (UniProt) |  | |
UniProt | |||||
Find proteins for Q08689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08689 Go to UniProtKB: Q08689 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q08689 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| human ACTH8 | D [auth F] | 8 | Homo sapiens | Mutation(s): 0 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01189 (Homo sapiens) Explore P01189 Go to UniProtKB: P01189 | |||||
PHAROS: P01189 GTEx: ENSG00000115138 | |||||
Entity Groups | |||||
| UniProt Group | P01189 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CMC Query on CMC | G [auth F] | CARBOXYMETHYL COENZYME *A C23 H38 N7 O18 P3 S OBUOSIHPWVNVJN-GRFIIANRSA-N |  | ||
| ACO Query on ACO | F [auth C] | ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N |  | ||
| G4P Query on G4P | E [auth A] | GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.81 ?
- R-Value Free: 0.297
- R-Value Work: 0.236
- R-Value Observed: 0.239
- Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 85.564 | ¦Á = 90 |
| b = 113.649 | ¦Â = 90 |
| c = 146.721 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2016-07-20 Deposition Author(s): Dong, J., Wang, S., York, J.D.
Revision History (Full details and data files)
- Version 1.0: 2016-07-20
Type: Initial release - Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary
