1I7L | pdb_00001i7l

CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX OF THE C DOMAIN OF SYNAPSIN II FROM RAT WITH ATP

PDB DOI: https://doi.org/10.2210/pdb1I7L/pdb

Classification: NEUROPEPTIDE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2001-03-09 Released: 2003-07-01
Deposition Author(s): Esser, L., Palnitkar, M., Deisenhofer, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.289 (Depositor), 0.288 (DCC)
R-Value Work:
0.220 (Depositor), 0.222 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

ATP Binding Independent of Metal Cations in Synapsin II

Esser, L., Palnitkar, M., Deisenhofer, J.

To be published.

Macromolecule Content

Total Structure Weight: 71.18 kDa
Atom Count: 5,181
Modeled Residue Count: 618
Deposited Residue Count: 618
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNAPSIN II	A, B	309	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q63537 (Rattus norvegicus) Explore Q63537 Go to UniProtKB: Q63537
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q63537
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.289 (Depositor), 0.288 (DCC)
R-Value Work: 0.220 (Depositor), 0.222 (DCC)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.275	α = 90
b = 121.275	β = 90
c = 165.891	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-07-01

Deposition Author(s):

Deisenhofer, J.

Revision History (Full details and data files)

Version 1.0: 2003-07-01
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2026-03-04
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.