8ITV | pdb_00008itv

KL2.1 in complex with CRM1-Ran-RanBP1

PDB DOI: https://doi.org/10.2210/pdb8ITV/pdb

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

Deposited: 2023-03-23 Released: 2024-03-27
Deposition Author(s): Sun, Q., Jian, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.224 (Depositor), 0.228 (DCC)
R-Value Work:
0.186 (Depositor), 0.191 (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

KL2.1 in complex with CRM1-Ran-RanBP1

Sun, Q., Jian, L.

To be published.

Macromolecule Content

Total Structure Weight: 159.11 kDa
Atom Count: 11,602
Modeled Residue Count: 1,324
Deposited Residue Count: 1,359
Unique protein chains: 3

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62826
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41920
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30822
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
Q73 (Subject of Investigation/LOI) Query on Q73 Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] MOL2 format, chain IA [auth C] mmCIF format, chain IA [auth C]	IA [auth C]	(3~{S},5~{R},6~{E},8~{Z},10~{R},12~{E},14~{E},16~{S})-3,16-bis(azanyl)-8,10,12-trimethyl-16-[(2~{S},4~{R},5~{S},6~{S})-5-methyl-4-oxidanyl-6-[(~{E})-prop-1-enyl]oxan-2-yl]-5-oxidanyl-hexadeca-6,8,12,14-tetraenoic acid C₂₈ H₄₆ N₂ O₅ ZMTRMZNTBHTQBT-XQYVQVJZSA-N		Interactions Focus chain IA [auth C] Interactions & Density Focus chain IA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth C] SDF format, chain Q [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain H [auth A] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	H [auth A], O [auth C], Q [auth C], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth C] Focus chain Q [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain H [auth A] Focus chain O [auth C] Focus chain Q [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain HA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain R [auth C] SDF format, chain X [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain R [auth C] MOL2 format, chain X [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain R [auth C] mmCIF format, chain X [auth C]	AA [auth C] CA [auth C] F [auth A] FA [auth C] HA [auth C] AA [auth C], CA [auth C], F [auth A], FA [auth C], HA [auth C], J [auth A], JA [auth C], R [auth C], X [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain HA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain R [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain HA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain R [auth C] Focus chain X [auth C]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain N [auth C] SDF format, chain P [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	BA [auth C] DA [auth C] E [auth A] EA [auth C] G [auth A] BA [auth C], DA [auth C], E [auth A], EA [auth C], G [auth A], I [auth A], L [auth C], N [auth C], P [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth C] Focus chain P [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth C] Focus chain P [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain GA [auth C] MOL2 format, chain GA [auth C] mmCIF format, chain GA [auth C]	GA [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain GA [auth C] Interactions & Density Focus chain GA [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [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]