5MQ4 | pdb_00005mq4

Crystal Structure of the leucine zipper of human PRKCBP1

PDB DOI: https://doi.org/10.2210/pdb5MQ4/pdb

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

Deposited: 2016-12-20 Released: 2017-01-25
Deposition Author(s): Krojer, T., Savitsky, P., Picaud, S., Newman, J., Tallant, C., Heroven, C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.208 (Depositor), 0.206 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5MQ4

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the leucine zipper of human PRKCBP1

Krojer, T., Savitsky, P., Picaud, S., Filippakopoulos, P.

To be published.

Macromolecule Content

Total Structure Weight: 91.61 kDa
Atom Count: 5,558
Modeled Residue Count: 674
Deposited Residue Count: 762
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase C-binding protein 1	A, B, C, D, E A, B, C, D, E, F	127	Homo sapiens	Mutation(s): 0 Gene Names: ZMYND8, KIAA1125, PRKCBP1, RACK7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULU4 (Homo sapiens) Explore Q9ULU4 Go to UniProtKB: Q9ULU4
PHAROS: Q9ULU4 GTEx: ENSG00000101040
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ULU4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain R [auth E] SDF format, chain O [auth D] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth F] MOL2 format, chain R [auth E] MOL2 format, chain O [auth D] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth F] mmCIF format, chain R [auth E] mmCIF format, chain O [auth D] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], O [auth D], R [auth E], U [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth D] Focus chain R [auth E] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth D] Focus chain R [auth E] Focus chain U [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth B] L [auth B] M [auth C] H [auth A], I [auth A], K [auth B], L [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], S [auth E], T [auth E], V [auth F], W [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.236 (Depositor), 0.236 (DCC)
R-Value Work: 0.208 (Depositor), 0.206 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.638	α = 90
b = 237.049	β = 90
c = 210.144	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
SHELXD	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Arrowsmith, C.H.

Filippakopoulos, P.

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.