6UK3 | pdb_00006uk3

Crystal Structure of S-adenosyl-L-homocysteine hydrolase from Acanthamoeba castellanii with bound NAD and Adenosine

PDB DOI: https://doi.org/10.2210/pdb6UK3/pdb

Classification: HYDROLASE
Organism(s): Acanthamoeba castellanii str. Neff
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-10-04 Released: 2019-10-16
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.161 (Depositor), 0.160 (DCC)
R-Value Work:
0.130 (Depositor), 0.130 (DCC)
R-Value Observed:
0.130 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of S-adenosyl-L-homocysteine hydrolase from Acanthamoeba castellanii with bound NAD and Adenosine

Romanaggi, C.T., Dranow, D.M., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 221.38 kDa
Atom Count: 17,784
Modeled Residue Count: 1,900
Deposited Residue Count: 1,940
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	485	Acanthamoeba castellanii str. Neff	Mutation(s): 0 Gene Names: ACA1_054200 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for L8H6B5 (Acanthamoeba castellanii (strain ATCC 30010 / Neff)) Explore L8H6B5 Go to UniProtKB: L8H6B5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L8H6B5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D]	E [auth A], J [auth B], R [auth C], X [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain X [auth D]
ADN (Subject of Investigation/LOI) Query on ADN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	F [auth A], K [auth B], S [auth C], Y [auth D]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain Y [auth D]
OXM Query on OXM Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain DA [auth D] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain U [auth C]	AA [auth D], DA [auth D], L [auth B], M [auth B], U [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain DA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain U [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D]	BA [auth D] CA [auth D] G [auth A] N [auth B] O [auth B] BA [auth D], CA [auth D], G [auth A], N [auth B], O [auth B], Q [auth B], T [auth C], V [auth C], Z [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain V [auth C] Focus chain Z [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	EA [auth D], H [auth A], P [auth B], W [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain EA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.161 (Depositor), 0.160 (DCC)
R-Value Work: 0.130 (Depositor), 0.130 (DCC)
R-Value Observed: 0.130 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36uk3

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.03	α = 90
b = 112.73	β = 114.725
c = 105.92	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ARP/wARP	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-10-16

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-10-16
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description