6QOY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lytic endopeptidase preproenzyme
A, B, C, D
199Lysobacter sp. XL1Mutation(s): 0 
Gene Names: alpA
UniProt
Find proteins for D2K8B3 (Lysobacter sp. (strain XL1))
Explore D2K8B3 
Go to UniProtKB:  D2K8B3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2K8B3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AES
Query on AES

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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
JAT
Query on JAT

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CA [auth D],
N [auth B],
V [auth C]
4-(2-azanylethyl)benzenesulfonic acid
C8 H11 N O3 S
RYBFWJVHZIKGQJ-UHFFFAOYSA-N
PGE
Query on PGE

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K [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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Q [auth B],
R [auth B],
Y [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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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
GOL
Query on GOL

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DA [auth D],
I [auth A],
J [auth A],
P [auth B],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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O [auth B],
W [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.855α = 90
b = 122.553β = 98.64
c = 78.988γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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