6IBI

Copper binding protein from Laetisaria arvalis (LaX325)

PDB DOI: https://doi.org/10.2210/pdb6IBI/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Laetisaria arvalis
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2018-11-30 Released: 2019-11-13
Deposition Author(s): Frandsen, K.E.H., Tandrup, T., Labourel, A., Haon, M., Berrin, J.-G., Lo Leggio, L.
Funding Organization(s): Novo Nordisk Foundation, The Carslberg Foundation, European Communitys Seventh Framework Programme

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.271
R-Value Work: 0.244
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 73.48 kDa
Atom Count: 5,546
Modelled Residue Count: 607
Deposited Residue Count: 620
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Auxiliary activity CAZyme	A, B, C, D	155	Laetisaria arvalis	Mutation(s): 0
UniProt
Find proteins for A0A4P9I8G4 (Waitea arvalis) Explore A0A4P9I8G4 Go to UniProtKB: A0A4P9I8G4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4P9I8G4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain L [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain W [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B]	FA [auth C], L [auth A], MA [auth D], N [auth A], W [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain L [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain W [auth B] Interactions & Density Focus chain FA [auth C] Focus chain L [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain W [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] F [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], F [auth A], G [auth A], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], LA [auth D], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain V [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain V [auth B]	EA [auth C], V [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain EA [auth C] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain V [auth B]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain GA [auth D] SDF format, chain O [auth B] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain X [auth C]	E [auth A], GA [auth D], O [auth B], X [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain GA [auth D] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain GA [auth D] Focus chain O [auth B] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.271
R-Value Work: 0.244
R-Value Observed: 0.245
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.599	α = 90
b = 84.635	β = 90
c = 127.319	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NF17SA0027704
The Carslberg Foundation	Denmark	CF16-0673 & CF17-0533
European Communitys Seventh Framework Programme	France	grant agreement 609398

Revision History (Full details and data files)

Version 1.0: 2019-11-13
Type: Initial release
Version 1.1: 2019-11-27
Changes: Derived calculations
Version 1.2: 2020-01-22
Changes: Database references
Version 1.3: 2020-03-04
Changes: Data collection, Database references
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary