7XB6 | pdb_00007xb6

Crystal structure of the O-carbamoyltransferase VtdB in complex with carbamoyl adenylate intermediate

PDB DOI: https://doi.org/10.2210/pdb7XB6/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-20 Released: 2023-03-22
Deposition Author(s): Zhang, H., Teng, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)

Starting Model: in silico
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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 O-carbamoyltransferase VtdB from Streptomyces sp. NO1W98 in complex with carbamoyladenylate

Zhang, H., Teng, Y.

To be published.

Macromolecule Content

Total Structure Weight: 265.1 kDa
Atom Count: 18,838
Modeled Residue Count: 2,388
Deposited Residue Count: 2,388
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbamoyltransferase	A, B, C, D	597	Streptomyces	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA0 (Subject of Investigation/LOI) Query on CA0 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]	5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine C₁₁ H₁₅ N₆ O₈ P CHSNPOFVFYPELH-KQYNXXCUSA-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]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-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]