3HKV | pdb_00003hkv

Human poly(ADP-ribose) polymerase 10, catalytic fragment in complex with an inhibitor 3-aminobenzamide

• PDB DOI: https://doi.org/10.2210/pdb3HKV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-05-26 Released: 2009-06-16 
• Deposition Author(s): Karlberg, T., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kotenyova, T., Kotzsch, A., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Sagemark, J., Schutz, P., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Human Poly(Adp-Ribose) Polymerase 10, Catalytic Fragment in Complex with an Inhibitor 3-Aminobenzamide

Karlberg, T., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kotenyova, T., Kotzsch, A., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Sagemark, J., Schutz, P., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 49.56 kDa 
• Atom Count: 3,306 
• Modeled Residue Count: 383 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 10	A, B	217	Homo sapiens	Mutation(s): 2  Gene Names: PARP10 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q53GL7 (Homo sapiens) Explore Q53GL7  Go to UniProtKB:  Q53GL7
PHAROS:  Q53GL7 GTEx:  ENSG00000178685

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3AB	G [auth A], I [auth B]	3-aminobenzamide C7 H8 N2 O GSCPDZHWVNUUFI-UHFFFAOYSA-N
PO4	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	F [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.242 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.38	α = 90
b = 97.38	β = 90
c = 121.16	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Karlberg, T., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kotenyova, T., Kotzsch, A., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Sagemark, J., Schutz, P., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-05-23
  Changes: Data collection
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description