8HRZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 

Starting Model: experimental
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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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
438Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55072
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NSFL1 cofactor p47
M, N, O, P, Q
M, N, O, P, Q, R, S, T, U, V, W, X
85Homo sapiensMutation(s): 0 
Gene Names: NSFL1CUBXN2C
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNZ2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.78α = 90
b = 178.85β = 119.8
c = 171.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2021R1A6A1A10044154
National Research Foundation (NRF, Korea)Korea, Republic Of2022R1C1C1004221

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