6ARH | pdb_00006arh

Crystal structure of Human NAL at a resolution of 1.6 Angstrom

PDB DOI: https://doi.org/10.2210/pdb6ARH/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-08-22 Released: 2018-08-22
Deposition Author(s): Pearce, F.G., Bundela, R., Keown, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.189 (Depositor), 0.199 (DCC)
R-Value Work:
0.164 (Depositor), 0.175 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ARH

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

Literature

Crystal structure of Human NAL at a resolution of 1.6 Angstrom

Pearce, F.G., Bundela, R., Keown, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 149.54 kDa
Atom Count: 10,729
Modeled Residue Count: 1,204
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylneuraminate lyase	A, B, C, D	338	Homo sapiens	Mutation(s): 0 Gene Names: NPL, C1orf13 EC: 4.1.3.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXD5 (Homo sapiens) Explore Q9BXD5 Go to UniProtKB: Q9BXD5
PHAROS: Q9BXD5 GTEx: ENSG00000135838
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BXD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D]	E [auth A] F [auth A] G [auth B] H [auth C] I [auth C] E [auth A], F [auth A], G [auth B], H [auth C], I [auth C], J [auth C], K [auth D], L [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189 (Depositor), 0.199 (DCC)
R-Value Work: 0.164 (Depositor), 0.175 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.988	α = 90
b = 106.897	β = 90
c = 127.027	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-08-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-08-22
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.