8HQ4 | pdb_00008hq4

B27 in complex with CRM1-Ran-RanBP1

PDB DOI: https://doi.org/10.2210/pdb8HQ4/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens, Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-12-13 Released: 2023-12-20
Deposition Author(s): Lei, Y., Sun, Q.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.210 (Depositor), 0.220 (DCC)
R-Value Work:
0.187 (Depositor), 0.200 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

B27 in complex with CRM1-Ran-RanBP1

Lei, Y., Sun, Q.

To be published.

Macromolecule Content

Total Structure Weight: 157.74 kDa
Atom Count: 11,404
Modeled Residue Count: 1,325
Deposited Residue Count: 1,359
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	A	216	Homo sapiens	Mutation(s): 2 Gene Names: RAN, ARA24, OK/SW-cl.81 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens) Explore P62826 Go to UniProtKB: P62826
PHAROS: P62826 GTEx: ENSG00000132341
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62826
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YRB1 isoform 1	B	140	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: YRB1, GI526_G0000915
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41920 Go to UniProtKB: P41920
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41920
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CRM1 isoform 1	C	1,003	Saccharomyces cerevisiae	Mutation(s): 11 Gene Names: CRM1, GI526_G0002640, PACBIOSEQ_LOCUS2878, PACBIOSEQ_LOCUS3002
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30822 Go to UniProtKB: P30822
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30822
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
M9R (Subject of Investigation/LOI) Query on M9R Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	3-[(4-fluorophenyl)carbonylamino]-4-[4-[3-(trifluoromethyl)phenyl]piperazin-1-yl]benzoic acid C₂₅ H₂₁ F₄ N₃ O₃ HDYCTRBNLDVBEL-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	E [auth A], K [auth C], L [auth C], M [auth C], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain J [auth C] SDF format, chain O [auth C] MOL2 format, chain G [auth C] MOL2 format, chain J [auth C] MOL2 format, chain O [auth C] mmCIF format, chain G [auth C] mmCIF format, chain J [auth C] mmCIF format, chain O [auth C]	G [auth C], J [auth C], O [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain J [auth C] Focus chain O [auth C] Interactions & Density Focus chain G [auth C] Focus chain J [auth C] Focus chain O [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C]	H [auth C], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain H [auth C] Focus chain I [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]