8OIO | pdb_00008oio

Crystal structure of the kelch domain of human KLHL12 in complex with PLEKHA4 peptide

PDB DOI: https://doi.org/10.2210/pdb8OIO/pdb

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

Deposited: 2023-03-23 Released: 2024-04-03
Deposition Author(s): Dalietou, E.V., Chen, Z., Ramdass, A.E., Manning, C., Richardson, W., Aitmakhanova, K., Platt, M., Pike, A.C.W., Fedorov, O., Brennan, P., Bullock, A.N.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of the kelch domain of human KLHL12 in complex with PLEKHA4 peptide

Dalietou, E.V., Chen, Z., Ramdass, A.E., Manning, C., Richardson, W., Aitmakhanova, K., Platt, M., Pike, A.C.W., Fedorov, O., Brennan, P., Bullock, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 135.84 kDa
Atom Count: 9,157
Modelled Residue Count: 1,155
Deposited Residue Count: 1,248
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like protein 12	A, B, C, D	301	Homo sapiens	Mutation(s): 0 Gene Names: KLHL12, C3IP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q53G59 (Homo sapiens) Explore Q53G59 Go to UniProtKB: Q53G59
PHAROS: Q53G59 GTEx: ENSG00000117153
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q53G59
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pleckstrin homology domain-containing family A member 4	E [auth F], F [auth G], G [auth H], H [auth E]	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H4M7 (Homo sapiens) Explore Q9H4M7 Go to UniProtKB: Q9H4M7
PHAROS: Q9H4M7 GTEx: ENSG00000105559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H4M7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C]	I [auth A], N [auth B], O [auth B], P [auth B], Q [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	K [auth B], L [auth B], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]