5GV5

Crystal structure of Candida antarctica Lipase B with active Ser105 modified with a phosphonate inhibitor

PDB DOI: https://doi.org/10.2210/pdb5GV5/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Moesziomyces antarcticus
Expression System: Aspergillus niger
Mutation(s): No

Deposited: 2016-09-02 Released: 2017-09-13
Deposition Author(s): Park, S.Y., Lee, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.229
R-Value Work: 0.171
R-Value Observed: 0.174

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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Structural and Experimental Evidence for the Enantiomeric Recognition toward a Bulky sec-Alcohol by Candida antarctica Lipase B

Park, K., Kim, S., Park, J., Joe, S., Min, B., Oh, J., Song, J., Park, S.Y., Park, S., Lee, H.

(2016) ACS Catal 6: 7458-7465

DOI: https://doi.org/10.1021/acscatal.6b02192

Macromolecule Content

Total Structure Weight: 270.94 kDa
Atom Count: 18,946
Modelled Residue Count: 2,524
Deposited Residue Count: 2,536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase B	A, B, C, D, E A, B, C, D, E, F, G, H	317	Moesziomyces antarcticus	Mutation(s): 0 EC: 3.1.1.3
UniProt
Find proteins for M9MDK9 (Pseudozyma antarctica (strain T-34)) Explore M9MDK9 Go to UniProtKB: M9MDK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M9MDK9
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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, K	4		N-Glycosylation	Interactions Focus chain I Focus chain K Interactions & Density Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G01361SX GlyCosmos: G01361SX GlyGen: G01361SX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, L, M, N, O J, L, M, N, O, P	2		N-Glycosylation	Interactions Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MSW Query on MSW Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain W [auth G] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain X [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth G] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth H]	Q [auth A] R [auth B] S [auth C] T [auth D] U [auth E] Q [auth A], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H]	[(1S)-2-(methoxycarbonylamino)-1-phenyl-ethoxy]-propyl-phosphinic acid C₁₃ H₂₀ N O₅ P LJRNVQUHAPUUFK-GFCCVEGCSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Interactions & Density Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.229
R-Value Work: 0.171
R-Value Observed: 0.174
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.462	α = 90
b = 123.222	β = 96.2
c = 150.316	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-09-13

Deposition Author(s):

Park, S.Y.

Lee, H.

Revision History (Full details and data files)

Version 1.0: 2017-09-13
Type: Initial release
Version 1.1: 2019-03-27
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary

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Help and Resources

5GV5

Crystal structure of Candida antarctica Lipase B with active Ser105 modified with a phosphonate inhibitor

Structural and Experimental Evidence for the Enantiomeric Recognition toward a Bulky sec-Alcohol by Candida antarctica Lipase B

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources