6RS6

X-ray crystal structure of LsAA9B

PDB DOI: https://doi.org/10.2210/pdb6RS6/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Panus similis
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2019-05-21 Released: 2019-09-11
Deposition Author(s): Frandsen, K.E.H., Tovborg, M., Poulsen, J.C.N., Johansen, K.S., Lo Leggio, L.
Funding Organization(s): Danish Agency for Science Technology and Innovation, Novo Nordisk Foundation, European Communitys Seventh Framework Programme, European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.182
R-Value Work: 0.137
R-Value Observed: 0.139

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 24.44 kDa
Atom Count: 1,944
Modelled Residue Count: 221
Deposited Residue Count: 221
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AA9	A	221	Panus similis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	G [auth A], H [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.182
R-Value Work: 0.137
R-Value Observed: 0.139
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.19	α = 90
b = 72.48	β = 90
c = 78.56	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Danish Agency for Science Technology and Innovation	Denmark	12-134922
Danish Agency for Science Technology and Innovation	Denmark	12-134923
Novo Nordisk Foundation	Denmark	NNF17SA0027704
European Communitys Seventh Framework Programme	Denmark	BioStruct-X (grant agreement N283570)
European Commission	Denmark	CF16-0673 - The Carlsberg Foundation
European Commission	Denmark	CF17-0533 - The Carlsberg Foundation
European Commission	France	AgreenSkills+ (Marie-Curie FP7 COFUND People Programme under grant agreement 609398)

Revision History (Full details and data files)

Version 1.0: 2019-09-11
Type: Initial release
Version 1.1: 2019-11-20
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2021-11-10
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 3.1: 2024-01-24
Changes: Data collection, Refinement description