5HDT | pdb_00005hdt

Human cohesin regulator Pds5B bound to a Wapl peptide

• PDB DOI: https://doi.org/10.2210/pdb5HDT/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2016-01-05 Released: 2016-03-09 
• Deposition Author(s): Ouyang, Z., Tomchick, D.R., Yu, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Structure of the human cohesin regulator Pds5 in complex with Wapl motif

Ouyang, Z., Tomchick, D.R., Yu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 263.38 kDa 
• Atom Count: 17,504 
• Modeled Residue Count: 2,163 
• Deposited Residue Count: 2,255 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sister chromatid cohesion protein PDS5 homolog B	A, B	1,111	Homo sapiens	Mutation(s): 1  Gene Names: PDS5B, APRIN, AS3, KIAA0979
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTI5 (Homo sapiens) Explore Q9NTI5  Go to UniProtKB:  Q9NTI5
PHAROS:  Q9NTI5 GTEx:  ENSG00000083642

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Wings apart-like protein homolog	C [auth E]	33	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z5K2 (Homo sapiens) Explore Q7Z5K2  Go to UniProtKB:  Q7Z5K2
PHAROS:  Q7Z5K2 GTEx:  ENSG00000062650

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	D [auth A], E [auth B]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.76	α = 90
b = 162.368	β = 90
c = 173.061	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Ouyang, Z., Tomchick, D.R., Yu, H.

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2020-10-14
  Changes: Structure summary
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary