7SU4 | pdb_00007su4

Dihydroneopterin aldolase (DHNA) Tyr53Phe from Yersinia pestis co-crystallized with 7,8-dihydroneopterin

PDB DOI: https://doi.org/10.2210/pdb7SU4/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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: 1.78 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.167 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (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) Tyr53Phe from Yersinia pestis co-crystallized with 7,8-dihydroneopterin

Bourne, C.R., Tan, A.

To be published.

Macromolecule Content

Total Structure Weight: 66.17 kDa
Atom Count: 4,490
Modeled Residue Count: 468
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8CZR7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NPR (Subject of Investigation/LOI) Query on NPR Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], L [auth C], M [auth D]	2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)-PTERIDINONE C₉ H₁₃ N₅ O₄ YQIFAMYNGGOTFB-NJGYIYPDSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth D] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth D] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth D] mmCIF format, chain H [auth A]	H [auth A], J [auth B], K [auth B], N [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D]