7SU8 | pdb_00007su8

DIHYDRONEOPTERIN ALDOLASE (DHNA) FROM YERSINIA PESTIS with alkylated Cys50 CO-CRYSTALLIZED with 7,8-dihydroneopterin

PDB DOI: https://doi.org/10.2210/pdb7SU8/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-16 Released: 2022-12-28
Deposition Author(s): Bourne, C.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.205 (Depositor), 0.213 (DCC)
R-Value Observed:
0.211 (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

DIHYDRONEOPTERIN ALDOLASE (DHNA) FROM YERSINIA PESTIS with alkylated Cys50 CO-CRYSTALLIZED with 7,8-dihydroneopterin

Bourne, C.R.

To be published.

Macromolecule Content

Total Structure Weight: 33.3 kDa
Atom Count: 1,963
Modeled Residue Count: 230
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydroneopterin aldolase	A, B	143	Yersinia pestis	Mutation(s): 0 Gene Names: y3531 EC: 4.1.2.25
UniProt
Find proteins for A0A5P8YJX5 (Yersinia pestis) Explore A0A5P8YJX5 Go to UniProtKB: A0A5P8YJX5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5P8YJX5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PH2 (Subject of Investigation/LOI) Query on PH2 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE C₇ H₉ N₅ O₂ CQQNNQTXUGLUEV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
NEN (Subject of Investigation/LOI) Query on NEN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	1-ETHYL-PYRROLIDINE-2,5-DIONE C₆ H₉ N O₂ GHAZCVNUKKZTLG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth B]	E [auth B], I [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth B] Focus chain I [auth B]