4GUK | pdb_00004guk

New crystal form structure of human NCS1

PDB DOI: https://doi.org/10.2210/pdb4GUK/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-29 Released: 2013-12-25
Deposition Author(s): Fan, C., Lolis, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.243 (Depositor), 0.242 (DCC)
R-Value Work:
0.201 (Depositor), 0.202 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

new crystal form structure of human NCS1

Fan, C., Lolis, E.

To be published.

Macromolecule Content

Total Structure Weight: 91.69 kDa
Atom Count: 6,402
Modeled Residue Count: 724
Deposited Residue Count: 760
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal calcium sensor 1	A, B [auth C], C [auth B], D	190	Homo sapiens	Mutation(s): 0 Gene Names: FLUP, FREQ, NCS1
UniProt & NIH Common Fund Data Resources
Find proteins for P62166 (Homo sapiens) Explore P62166 Go to UniProtKB: P62166
PHAROS: P62166 GTEx: ENSG00000107130
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P2G Query on P2G Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain IA [auth D] SDF format, chain S [auth C] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain S [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain S [auth C] mmCIF format, chain AA [auth B]	AA [auth B], BA [auth B], IA [auth D], S [auth C]	(2S,4R,6R,6AS)-4-(2-AMINO-6-OXO-1,6-DIHYDROPURIN-9-YL)-6-(HYDROXYMETHYL)-TETRAHYDROFURO[3,4-D][1,3]DIOXOL-2-YLPHOSPHONI C ACID C₁₁ H₁₄ N₅ O₈ P GKAPYWCOOQBBHV-KXSYMAMXSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain IA [auth D] Focus chain S [auth C] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain IA [auth D] Focus chain S [auth C]
P3G Query on P3G Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	3,6,9,12,15-PENTAOXAHEPTADECANE C₁₂ H₂₆ O₅ HYDWALOBQJFOMS-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain E [auth A] SDF format, chain JA [auth D] SDF format, chain X [auth B] SDF format, chain N [auth C] SDF format, chain KA [auth D] SDF format, chain F [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain N [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain F [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain N [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain F [auth A]	CA [auth B] E [auth A] F [auth A] JA [auth D] KA [auth D] CA [auth B], E [auth A], F [auth A], JA [auth D], KA [auth D], N [auth C], X [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain N [auth C] Focus chain X [auth B] Interactions & Density Focus chain CA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain N [auth C] Focus chain X [auth B]
ALA Query on ALA Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain Z [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth A], HA [auth D], I [auth A], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain Z [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain Z [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain U [auth B] SDF format, chain P [auth C] SDF format, chain L [auth A] SDF format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain U [auth B] MOL2 format, chain P [auth C] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain U [auth B] mmCIF format, chain P [auth C] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth D]	EA [auth D] FA [auth D] GA [auth D] J [auth A] K [auth A] EA [auth D], FA [auth D], GA [auth D], J [auth A], K [auth A], L [auth A], P [auth C], Q [auth C], R [auth C], U [auth B], V [auth B], W [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain M [auth A] SDF format, chain T [auth C] SDF format, chain LA [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain T [auth C] MOL2 format, chain LA [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain T [auth C] mmCIF format, chain LA [auth D]	DA [auth B], LA [auth D], M [auth A], T [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain LA [auth D] Focus chain M [auth A] Focus chain T [auth C] Interactions & Density Focus chain DA [auth B] Focus chain LA [auth D] Focus chain M [auth A] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.243 (Depositor), 0.242 (DCC)
R-Value Work: 0.201 (Depositor), 0.202 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.987	α = 90
b = 54.987	β = 90
c = 213.954	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

Fan, C.

Lolis, E.

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2019-01-23
Changes: Data collection, Database references, Structure summary
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2024-04-03
Changes: Refinement description