4QDV | pdb_00004qdv

Dcps in complex with covalent ligand

PDB DOI: https://doi.org/10.2210/pdb4QDV/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-14 Released: 2015-05-20
Deposition Author(s): Liu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.250 (Depositor), 0.270 (DCC)
R-Value Work:
0.205 (Depositor), 0.220 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Dcps in complex with covalent ligands targeting Tyrosines

Liu, S.

To be published.

Macromolecule Content

Total Structure Weight: 156.09 kDa
Atom Count: 9,663
Modeled Residue Count: 1,156
Deposited Residue Count: 1,348
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
m7GpppX diphosphatase	A, B, C, D	337	Homo sapiens	Mutation(s): 0 Gene Names: DCPS, DCS1, HINT5, HSPC015 EC: 3.6.1.59
UniProt & NIH Common Fund Data Resources
Find proteins for Q96C86 (Homo sapiens) Explore Q96C86 Go to UniProtKB: Q96C86
PHAROS: Q96C86 GTEx: ENSG00000110063
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96C86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
30U Query on 30U Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain N [auth D]	E [auth A], N [auth D]	4-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid C₁₅ H₁₄ N₄ O₄ S AVKNBINNLVQZGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain N [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	F [auth A] G [auth A] H [auth A] I [auth B] J [auth B] F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.250 (Depositor), 0.270 (DCC)
R-Value Work: 0.205 (Depositor), 0.220 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.09	α = 90
b = 105.51	β = 90
c = 140	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
BUSTER	refinement
autoPROC	data scaling
Aimless	data scaling
BUSTER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-05-20

Deposition Author(s):

Liu, S.

Revision History (Full details and data files)

Version 1.0: 2015-05-20
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-03-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary

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Help and Resources

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Dcps in complex with covalent ligand

Dcps in complex with covalent ligands targeting Tyrosines

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations