3T6V

Crystal Structure of Laccase from Steccherinum ochraceum

PDB DOI: https://doi.org/10.2210/pdb3T6V/pdb

Classification: OXIDOREDUCTASE
Organism(s): Steccherinum ochraceum
Mutation(s): No

Deposited: 2011-07-29 Released: 2012-04-18
Deposition Author(s): Ferraroni, M., Briganti, F., Matera, I., Kolomytseva, M., Golovleva, L., Scozzafava, A., Chernykh, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.241
R-Value Work: 0.181
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 163 kDa
Atom Count: 12,647
Modelled Residue Count: 1,485
Deposited Residue Count: 1,485
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laccase	A, B, C	495	Steccherinum ochraceum	Mutation(s): 0
UniProt
Find proteins for I1SB14 (Steccherinum ochraceum) Explore I1SB14 Go to UniProtKB: I1SB14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I1SB14
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	D, E, F, G, H	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain JA [auth C] MOL2 format, chain JA [auth C]	JA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain JA [auth C] Interactions & Density Focus chain JA [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain V [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain V [auth B]	FA [auth C] GA [auth C] M [auth A] N [auth A] O [auth A] FA [auth C], GA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain Q [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] HA [auth C] IA [auth C] Q [auth A] W [auth B] AA [auth B], HA [auth C], IA [auth C], Q [auth A], 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 HA [auth C] Focus chain IA [auth C] Focus chain Q [auth A] 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 HA [auth C] Focus chain IA [auth C] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] 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 R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] 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 R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] I [auth A] BA [auth C], CA [auth C], DA [auth C], EA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B], U [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.241
R-Value Work: 0.181
R-Value Observed: 0.184
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.535	α = 90
b = 140.662	β = 90
c = 174.178	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-04-18
Type: Initial release
Version 1.1: 2012-10-03
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary