5NNS

Crystal structure of HiLPMO9B

PDB DOI: https://doi.org/10.2210/pdb5NNS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Heterobasidion irregulare TC 32-1
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2017-04-10 Released: 2018-05-16
Deposition Author(s): Dimarogona, M., Sandgren, M.
Funding Organization(s): Vinnova

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.251
R-Value Work: 0.200
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 50.68 kDa
Atom Count: 3,854
Modelled Residue Count: 450
Deposited Residue Count: 450
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 61, 2 protein	A, B	225	Heterobasidion irregulare TC 32-1	Mutation(s): 0 Gene Names: GH61B, HETIRDRAFT_166613
UniProt
Find proteins for W4KMP1 (Heterobasidion irregulare (strain TC 32-1)) Explore W4KMP1 Go to UniProtKB: W4KMP1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W4KMP1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	C [auth A], D [auth A], Q [auth B], R [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain Q [auth B] Focus chain R [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain F [auth A] SDF format, chain W [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain F [auth A] MOL2 format, chain W [auth B]	AA [auth B] BA [auth B] F [auth A] G [auth A] H [auth A] AA [auth B], BA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
AKR Query on AKR Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A]	CA [auth B], DA [auth B], EA [auth B], N [auth A], O [auth A]	ACRYLIC ACID C₃ H₄ O₂ NIXOWILDQLNWCW-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain N [auth A] Focus chain O [auth A]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain S [auth B]	E [auth A], S [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain S [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A]	P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.251
R-Value Work: 0.200
R-Value Observed: 0.203
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.695	α = 90
b = 46.375	β = 103.23
c = 86.492	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Dimarogona, M.

Sandgren, M.

Funding Organization	Location	Grant Number
Vinnova	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2018-12-05
Changes: Data collection, Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary