5KKP | pdb_00005kkp

Crystal Structure of Human Pseudouridylate Synthase 7

• PDB DOI: https://doi.org/10.2210/pdb5KKP/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-22 Released: 2016-08-17 
• Deposition Author(s): DONG, A., ZENG, H., WALKER, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.263 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal Structure of Human Pseudouridylate Synthase 7

ZENG, H., DONG, A., WALKER, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.31 kDa 
• Atom Count: 4,027 
• Modeled Residue Count: 509 
• Deposited Residue Count: 563 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudouridylate synthase 7	A	563	Homo sapiens	Mutation(s): 0  Gene Names: PUS7, KIAA1897 EC: 5.4.99
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PZ0 (Homo sapiens) Explore Q96PZ0  Go to UniProtKB:  Q96PZ0
PHAROS:  Q96PZ0 GTEx:  ENSG00000091127

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	C [auth A], D [auth A], E [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.263 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35KKP

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.356	α = 90
b = 73.4	β = 90
c = 138.179	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
Coot	model building
HKL-3000	data reduction
RESOLVE	phasing
WARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): DONG, A., ZENG, H., WALKER, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary