8ZRS | pdb_00008zrs

Crystal structure of Skd3, AAA+ only

PDB DOI: https://doi.org/10.2210/pdb8ZRS/pdb

Classification: CHAPERONE
Organism(s): Danio rerio
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-06-05 Released: 2025-06-11
Deposition Author(s): Lee, S., Lee, C.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free:
0.284 (Depositor), 0.291 (DCC)
R-Value Work:
0.229 (Depositor), 0.274 (DCC)
R-Value Observed:
0.231 (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

Crystal structure of Skd3, AAA+ only

Lee, S., Lee, C.

To be published.

Macromolecule Content

Total Structure Weight: 500.96 kDa
Atom Count: 28,287
Modeled Residue Count: 3,452
Deposited Residue Count: 4,344
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caseinolytic peptidase B protein homolog	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	362	Danio rerio	Mutation(s): 0 Gene Names: clpb
UniProt
Find proteins for A0A8M3AT32 (Danio rerio) Explore A0A8M3AT32 Go to UniProtKB: A0A8M3AT32
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8M3AT32
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain W [auth K] SDF format, chain V [auth J] SDF format, chain U [auth I] SDF format, chain T [auth H] SDF format, chain S [auth G] SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain X [auth L] MOL2 format, chain W [auth K] MOL2 format, chain V [auth J] MOL2 format, chain U [auth I] MOL2 format, chain T [auth H] MOL2 format, chain S [auth G] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain X [auth L] mmCIF format, chain W [auth K] mmCIF format, chain V [auth J] mmCIF format, chain U [auth I] mmCIF format, chain T [auth H] mmCIF format, chain S [auth G] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free: 0.284 (Depositor), 0.291 (DCC)
R-Value Work: 0.229 (Depositor), 0.274 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.857	α = 90
b = 172.407	β = 120
c = 140.866	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

Lee, S.

Lee, C.

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021M3A9G8022417
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1A2C2009550