Download MendeleyCrystal structure of RPE65 in complex with MB-003 and palmitate
Bassetto, M.To be published.
8DOC
Crystal structure of RPE65 in complex with compound 16e and palmitate
- PDB DOI: https://doi.org/10.2210/pdb8DOC/pdb
- Classification: HYDROLASE
- Organism(s): Bos taurus
- Mutation(s): Yes
- Deposited: 2022-07-12 Released: 2023-05-24
- Funding Organization(s): Department of Veterans Affairs (VA, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.211
- R-Value Work: 0.178
- R-Value Observed: 0.179
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Retinoid isomerohydrolase | A | 533 | Bos taurus | Mutation(s): 1 Gene Names: RPE65 EC: 3.1.1.64 (PDB Primary Data), 5.3.3.22 (PDB Primary Data) |  |
UniProt | |||||
Find proteins for Q28175 (Bos taurus) Explore Q28175 Go to UniProtKB: Q28175 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q28175 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SYL (Subject of Investigation/LOI) Query on SYL | E [auth A] | (1R)-1-[3-(cyclohexylmethoxy)phenyl]-3-(methylamino)propan-1-ol C17 H27 N O2 ZUJMXLRQVDCTHJ-QGZVFWFLSA-N |  | Ligand Interaction | |
| PLM (Subject of Investigation/LOI) Query on PLM | D [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N |  | Ligand Interaction | |
| CXS Query on CXS | C [auth A] | 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N |  | Ligand Interaction | |
| FE2 (Subject of Investigation/LOI) Query on FE2 | B [auth A] | FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.211
- R-Value Work: 0.178
- R-Value Observed: 0.179
- Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 176.82 | α = 90 |
| b = 176.82 | β = 90 |
| c = 86.19 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| XSCALE | data scaling |
| REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-05-24 Deposition Author(s): Bassetto, M., Kiser, P.D.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Department of Veterans Affairs (VA, United States) | -- |
Revision History (Full details and data files)
- Version 1.0: 2023-05-24
Type: Initial release
