7SU7 | pdb_00007su7

Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with product

PDB DOI: https://doi.org/10.2210/pdb7SU7/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli
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: 2.09 Å
R-Value Free:
0.236 (Depositor), 0.238 (DCC)
R-Value Work:
0.179 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (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

Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with product

Bourne, C.R.

To be published.

Macromolecule Content

Total Structure Weight: 65.98 kDa
Atom Count: 4,160
Modeled Residue Count: 472
Deposited Residue Count: 572
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, C, D	143	Yersinia pestis	Mutation(s): 0 Gene Names: y3531 EC: 4.1.2.25
UniProt
Find proteins for Q8CZR7 (Yersinia pestis) Explore Q8CZR7 Go to UniProtKB: Q8CZR7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8CZR7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B]	G [auth B], I [auth C], J [auth C], K [auth D]	2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE C₇ H₉ N₅ O₂ CQQNNQTXUGLUEV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], L [auth D], M [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth D] Focus chain M [auth D]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]