5QBL | pdb_00005qbl

Crystal structure of Endothiapepsin-NAT17-347147 complex

PDB DOI: https://doi.org/10.2210/pdb5QBL/pdb
Deposition Group: G_1002039 | Explore G_1002039

Classification: HYDROLASE
Organism(s): Cryphonectria parasitica
Mutation(s): No

Deposited: 2017-08-04 Released: 2020-04-22
Deposition Author(s): Huschmann, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.197 (Depositor), 0.198 (DCC)
R-Value Work:
0.162 (Depositor), 0.164 (DCC)
R-Value Observed:
0.164 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of Endothiapepsin

Huschmann, F.U., Weiss, M.S., Mueller, U., Haustedt, L.O., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 34.85 kDa
Atom Count: 2,867
Modeled Residue Count: 330
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothiapepsin	A	330	Cryphonectria parasitica	Mutation(s): 0 EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838 Go to UniProtKB: P11838
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11838
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D9D Query on D9D Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	(1S,2S,3S,4R,5R)-2-({[5-(hydroxymethyl)furan-2-yl]methyl}amino)-4-(morpholin-4-yl)-6,8-dioxabicyclo[3.2.1]octan-3-ol C₁₆ H₂₄ N₂ O₆ QPKSUNGYGHKTGL-DGXTUMSLSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.197 (Depositor), 0.198 (DCC)
R-Value Work: 0.162 (Depositor), 0.164 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.479	α = 90
b = 73.724	β = 110.23
c = 53.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-04-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-04-22
Type: Initial release
Version 1.1: 2021-11-17
Changes: Database references, Structure summary
Version 1.2: 2024-10-30
Changes: Data collection, Structure summary

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