7XQA

Orf1-glycine complex

PDB DOI: https://doi.org/10.2210/pdb7XQA/pdb

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

Deposited: 2022-05-07 Released: 2023-05-31
Deposition Author(s): Wang, Y.L., Li, T.L.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.208
R-Value Work: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry

Wang, Y.L., Chang, C.Y., Hsu, N.S., Lo, I.W., Lin, K.H., Chen, C.L., Chang, C.F., Wang, Z.C., Ogasawara, Y., Dairi, T., Maruyama, C., Hamano, Y., Li, T.L.

(2023) Nat Commun 14: 2528

DOI: https://doi.org/10.1038/s41467-023-38218-w

Macromolecule Content

Total Structure Weight: 447.55 kDa
Atom Count: 32,835
Modelled Residue Count: 3,850
Deposited Residue Count: 4,096
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-formimidoyl fortimicin A synthase	A, B, C, D, E A, B, C, D, E, F, G	512	Streptomyces luteocolor	Mutation(s): 0
UniProt
Find proteins for A0A125SZC1 (Streptomyces luteocolor) Explore A0A125SZC1 Go to UniProtKB: A0A125SZC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A125SZC1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-formimidoyl fortimicin A synthase	H	512	Streptomyces luteocolor	Mutation(s): 0
UniProt
Find proteins for A0A125SZC1 (Streptomyces luteocolor) Explore A0A125SZC1 Go to UniProtKB: A0A125SZC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A125SZC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain I [auth A]	I [auth A] L [auth B] N [auth C] P [auth D] R [auth E] I [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], W [auth G], Y [auth H]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain W [auth G] Focus chain Y [auth H]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H]	J [auth A] K [auth A] M [auth B] O [auth C] Q [auth D] J [auth A], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], V [auth F], X [auth G], Z [auth H]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]