7KF3 | pdb_00007kf3

Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose

PDB DOI: https://doi.org/10.2210/pdb7KF3/pdb

Classification: LYASE
Organism(s): Brucella abortus 2308
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-13 Released: 2020-11-04
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.174 (Depositor), 0.170 (DCC)
R-Value Observed:
0.175 (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 GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 173.34 kDa
Atom Count: 12,289
Modeled Residue Count: 1,448
Deposited Residue Count: 1,476
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-mannose 4,6-dehydratase	A, B, C, D	369	Brucella abortus 2308	Mutation(s): 0 Gene Names: gmd, BAB1_0545 EC: 4.2.1.47
UniProt
Find proteins for Q2YMP3 (Brucella abortus (strain 2308)) Explore Q2YMP3 Go to UniProtKB: Q2YMP3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2YMP3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
GDR (Subject of Investigation/LOI) Query on GDR Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE C₁₆ H₂₅ N₅ O₁₅ P₂ LQEBEXMHBLQMDB-GDJBGNAASA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]