6W4N | pdb_00006w4n

Co-crystal structure of Pd_dinase with probe glycine-propargylglycine-AOMK

PDB DOI: https://doi.org/10.2210/pdb6W4N/pdb

Classification: HYDROLASE
Organism(s): Parabacteroides distasonis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-11 Released: 2021-03-17
Deposition Author(s): Xu, J.H., Solania, A., Wolan, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.229 (Depositor), 0.233 (DCC)
R-Value Work:
0.207 (Depositor), 0.211 (DCC)
R-Value Observed:
0.209 (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

Co-crystal structure of Pd_dinase with probe glycine-propargylglycine-AOMK

Xu, J.H., Solania, A., Wolan, D.W.

To be published.

Macromolecule Content

Total Structure Weight: 276.85 kDa
Atom Count: 17,389
Modeled Residue Count: 2,124
Deposited Residue Count: 2,406
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase	A, B, C, D, E A, B, C, D, E, F	401	Parabacteroides distasonis	Mutation(s): 0 Gene Names: DW188_02780, DW692_01025, DW700_01025, DW808_17970, DW814_08450, DW867_06285, DW984_01045, DW998_13650, DWW19_04025, DWY54_02375... DW188_02780, DW692_01025, DW700_01025, DW808_17970, DW814_08450, DW867_06285, DW984_01045, DW998_13650, DWW19_04025, DWY54_02375, DWZ58_02465, DXD05_07510
UniProt
Find proteins for A6LE66 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LE66 Go to UniProtKB: A6LE66
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6LE66
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SWJ (Subject of Investigation/LOI) Query on SWJ Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain S [auth E] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain V [auth F] MOL2 format, chain S [auth E] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain V [auth F] mmCIF format, chain S [auth E] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] M [auth C] P [auth D] S [auth E] G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]	2-azanyl-~{N}-[(3~{S})-2-oxidanylidenehex-5-yn-3-yl]ethanamide C₈ H₁₂ N₂ O₂ YHGRTOPUPRQLPX-ZETCQYMHSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth B] L [auth B] N [auth C] H [auth A], I [auth A], K [auth B], L [auth B], N [auth C], O [auth C], Q [auth D], R [auth D], T [auth E], U [auth E], W [auth F], X [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.229 (Depositor), 0.233 (DCC)
R-Value Work: 0.207 (Depositor), 0.211 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.113	α = 90
b = 138.613	β = 90
c = 220.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Xu, J.H.

Solania, A.

Wolan, D.W.

Revision History (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary