5GV5 | pdb_00005gv5

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 (Depositor), 0.236 (DCC)
R-Value Work:
0.171 (Depositor), 0.182 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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
Modeled Residue Count: 2,524
Deposited Residue Count: 2,536
Unique protein chains: 1

Macromolecules

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| 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 P41365 (Pseudozyma antarctica) Explore P41365 Go to UniProtKB: P41365
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41365
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	D 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 X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth A] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth A]	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 (Depositor), 0.236 (DCC)
R-Value Work: 0.171 (Depositor), 0.182 (DCC)
R-Value Observed: 0.174 (Depositor)

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

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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
Version 2.1: 2024-11-06
Changes: Data collection, Database references, Structure summary