1AK0

P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG

• PDB DOI: https://doi.org/10.2210/pdb1AK0/pdb

• Classification: ENDONUCLEASE
• Organism(s): Penicillium citrinum
• Mutation(s): No 


• Deposited: 1997-05-28 Released: 1997-12-03 
• Deposition Author(s): Romier, C., Suck, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.82 kDa 
• Atom Count: 2,313 
• Modelled Residue Count: 264 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P1 NUCLEASE	A	270	Penicillium citrinum	Mutation(s): 0  EC: 3.1.30.1
UniProt
Find proteins for P24289 (Penicillium citrinum) Explore P24289  Go to UniProtKB:  P24289

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADS	I [auth A]	ADENOSINE-5'-(DITHIO)PHOSPHATE C10 H14 N5 O5 P S2 RPDDEEQJNPPYRG-CPTYKQRNSA-N
THS	J [auth A], K [auth A], L [auth A]	THYMIDINE-5'-(DITHIO)PHOSPHATE C10 H15 N2 O6 P S2 KMPXQZWMYQHTNT-XLPZGREQSA-N
NAG	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.98	α = 90
b = 74.04	β = 90
c = 102.13	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-12-03 
Deposition Author(s): Romier, C., Suck, D.

Revision History  

• Version 1.0: 1997-12-03
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary