8HRZ | pdb_00008hrz

Crystal structure of the p97-N/D1 hexamer in complex with six p47-UBX domains

PDB DOI: https://doi.org/10.2210/pdb8HRZ/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-12-16 Released: 2023-12-20
Deposition Author(s): Nguyen, T.Q., Kang, W.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.256 (Depositor), 0.257 (DCC)
R-Value Work:
0.213 (Depositor), 0.214 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the p97-N/D1 hexmaer in complex with six p47-UBX domains

Nguyen, T.Q., Kang, W.

(2024) J Korean Chem Soc 68: 25-31

DOI: https://doi.org/10.5012/jkcs.2024.68.1.25

Macromolecule Content

Total Structure Weight: 706.88 kDa
Atom Count: 49,084
Modeled Residue Count: 6,252
Deposited Residue Count: 6,276
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transitional endoplasmic reticulum ATPase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	438	Homo sapiens	Mutation(s): 2 Gene Names: VCP EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens) Explore P55072 Go to UniProtKB: P55072
PHAROS: P55072 GTEx: ENSG00000165280
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55072
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NSFL1 cofactor p47	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W, X	85	Homo sapiens	Mutation(s): 0 Gene Names: NSFL1C, UBXN2C
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNZ2 (Homo sapiens) Explore Q9UNZ2 Go to UniProtKB: Q9UNZ2
PHAROS: Q9UNZ2 GTEx: ENSG00000088833
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UNZ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth J] SDF format, chain JA [auth L] SDF format, chain Y [auth A] SDF format, chain Z [auth B] SDF format, chain IA [auth K] SDF format, chain CA [auth E] SDF format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain JA [auth L] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain IA [auth K] MOL2 format, chain CA [auth E] MOL2 format, chain AA [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain HA [auth J] mmCIF format, chain JA [auth L] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain IA [auth K] mmCIF format, chain CA [auth E] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth D] CA [auth E] DA [auth F] EA [auth G] AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth J], IA [auth K], JA [auth L], Y [auth A], Z [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain Y [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256 (Depositor), 0.257 (DCC)
R-Value Work: 0.213 (Depositor), 0.214 (DCC)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.78	α = 90
b = 178.85	β = 119.8
c = 171.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Nguyen, T.Q.

Kang, W.

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1A6A1A10044154
National Research Foundation (NRF, Korea)	Korea, Republic Of	2022R1C1C1004221

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release
Version 1.1: 2024-05-29
Changes: Database references