1N9E | pdb_00001n9e

Crystal structure of Pichia pastoris Lysyl Oxidase PPLO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.187 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history

Literature

The Crystal Structure of Pichia pastoris Lysyl Oxidase

Duff, A.P.Cohen, A.E.Ellis, P.J.Kuchar, J.A.Langley, D.B.Shepard, E.M.Dooley, D.M.Freeman, H.C.Guss, J.M.

(2003) Biochemistry 42: 15148-15157

  • DOI: https://doi.org/10.1021/bi035338v
  • Primary Citation Related Structures: 
    1N9E

  • PubMed Abstract: 

    Pichia pastoris lysyl oxidase (PPLO) is unique among the structurally characterized copper amine oxidases in being able to oxidize the side chain of lysine residues in polypeptides. Remarkably, the yeast PPLO is nearly as effective in oxidizing a mammalian tropoelastin substrate as is a true mammalian lysyl oxidase isolated from bovine aorta. Thus, PPLO is functionally related to the copper-containing lysyl oxidases despite the lack of any significant sequence similarity with these enzymes. The structure of PPLO has been determined at 1.65 A resolution. PPLO is a homodimer in which each subunit contains a Type II copper atom and a topaquinone cofactor (TPQ) formed by the posttranslational modification of a tyrosine residue. While PPLO has tertiary and quaternary topologies similar to those found in other quinone-containing copper amine oxidases, its active site is substantially more exposed and accessible. The structural elements that are responsible for the accessibility of the active site are identified and discussed.


  • Organizational Affiliation
    • School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW, Australia.

Macromolecule Content 

  • Total Structure Weight: 367.7 kDa 
  • Atom Count: 28,271 
  • Modeled Residue Count: 2,940 
  • Deposited Residue Count: 3,148 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LYSYL OXIDASE
A, B, C, D
787Komagataella pastorisMutation(s): 0 
EC: 1.4.3.13 (PDB Primary Data), 1.4.3 (UniProt)
UniProt
Find proteins for Q96X16 (Komagataella pastoris)
Explore Q96X16 
Go to UniProtKB:  Q96X16
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96X16
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth D]
BB [auth D]
I [auth A]
J [auth A]
K [auth A]
AB [auth D],
BB [auth D],
I [auth A],
J [auth A],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
MA [auth C],
NA [auth C],
W [auth B],
X [auth B],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
DA [auth B]
EA [auth B]
FA [auth B]
FB [auth D]
GA [auth B]
DA [auth B],
EA [auth B],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
HA [auth B],
HB [auth D],
IA [auth B],
IB [auth D],
JA [auth B],
JB [auth D],
KB [auth D],
LB [auth D],
P [auth A],
Q [auth A],
R [auth A],
RA [auth C],
S [auth A],
SA [auth C],
T [auth A],
TA [auth C],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
WA [auth C],
XA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU

Query on CU



Download:Ideal Coordinates CCD File
AA [auth B],
CB [auth D],
M [auth A],
OA [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
BA [auth B]
CA [auth B]
DB [auth D]
EB [auth D]
N [auth A]
BA [auth B],
CA [auth B],
DB [auth D],
EB [auth D],
N [auth A],
O [auth A],
PA [auth C],
QA [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPQ
Query on TPQ
A, B, C, D
L-PEPTIDE LINKINGC9 H9 N O5TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.187 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 248.442α = 90
b = 121.125β = 124.64
c = 151.841γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2014-10-29
    Changes: Derived calculations
  • Version 1.4: 2018-02-07
    Changes: Advisory, Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary