6QOY | pdb_00006qoy

Crystal structure of L1 protease Lysobacter sp. XL1 in complex with AEBSF

PDB DOI: https://doi.org/10.2210/pdb6QOY/pdb

Classification: HYDROLASE
Organism(s): Lysobacter sp. XL1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-02-13 Released: 2019-12-25
Deposition Author(s): Gabdulkhakov, A., Tishchenko, S., Kudryakova, I., Afoshin, A., Vasilyeva, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.240 (Depositor), 0.233 (DCC)
R-Value Work:
0.200 (Depositor), 0.193 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Serine bacteriolytic protease L1 of Lysobacter sp. XL1 complexed with protease inhibitor AEBSF: features of interaction

Kudryakova, I., Gabdulkhakov, A., Tishchenko, S., Afoshin, A., Vasilyeva, N.

(2019) Process Biochem

DOI: https://doi.org/10.1016/j.procbio.2019.02.013

Macromolecule Content

Total Structure Weight: 82.58 kDa
Atom Count: 6,283
Modeled Residue Count: 796
Deposited Residue Count: 796
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lytic endopeptidase preproenzyme	A, B, C, D	199	Lysobacter sp. XL1	Mutation(s): 0 Gene Names: alpA
UniProt
Find proteins for D2K8B3 (Lysobacter sp. (strain XL1)) Explore D2K8B3 Go to UniProtKB: D2K8B3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2K8B3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AES Query on AES Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain H [auth A] SDF format, chain U [auth C] SDF format, chain M [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain U [auth C] MOL2 format, chain M [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain U [auth C] mmCIF format, chain M [auth B]	BA [auth D], H [auth A], M [auth B], U [auth C]	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE C₈ H₁₀ F N O₂ S MGSKVZWGBWPBTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain H [auth A] Focus chain M [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain H [auth A] Focus chain M [auth B] Focus chain U [auth C]
JAT Query on JAT Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain N [auth B] SDF format, chain V [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C]	CA [auth D], N [auth B], V [auth C]	4-(2-azanylethyl)benzenesulfonic acid C₈ H₁₁ N O₃ S RYBFWJVHZIKGQJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain N [auth B] Focus chain V [auth C]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain Y [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C]	Q [auth B], R [auth B], Y [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain S [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	AA [auth D] E [auth A] F [auth A] G [auth A] L [auth B] AA [auth D], E [auth A], F [auth A], G [auth A], L [auth B], S [auth B], T [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C]	DA [auth D], I [auth A], J [auth A], P [auth B], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain X [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain W [auth C] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] mmCIF format, chain O [auth B] mmCIF format, chain W [auth C]	O [auth B], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth B] Focus chain W [auth C] Interactions & Density Focus chain O [auth B] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240 (Depositor), 0.233 (DCC)
R-Value Work: 0.200 (Depositor), 0.193 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.855	α = 90
b = 122.553	β = 98.64
c = 78.988	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-12-25
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary