8AGY | pdb_00008agy

The Corramycin phosphotransferase in complex with Corramycin

PDB DOI: https://doi.org/10.2210/pdb8AGY/pdb

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

Deposited: 2022-07-20 Released: 2023-08-16
Deposition Author(s): Adam, S., Mueller, R., Koehnke, J.
Funding Organization(s): Helmholtz Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.194 (Depositor), 0.189 (DCC)
R-Value Work:
0.175 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

The Corramycin phosphotransferase in complex with Corramycin

Adam, S., Mueller, R., Koehnke, J.

To be published.

Macromolecule Content

Total Structure Weight: 42.39 kDa
Atom Count: 3,272
Modeled Residue Count: 356
Deposited Residue Count: 376
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corramycin phosphotransferase	A	366	Corallococcus coralloides	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Corramycin	B	10	Corallococcus coralloides	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HVA Query on HVA	B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃		VAL
MEA Query on MEA	B	L-PEPTIDE LINKING	C₁₀ H₁₃ N O₂		PHE
OGC Query on OGC	B	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₃		HIS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002426 Query on PRD_002426	B	Corramycin	Peptide-like / Antibiotic, Antimicrobial		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.194 (Depositor), 0.189 (DCC)
R-Value Work: 0.175 (Depositor), 0.173 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.964	α = 90
b = 67.116	β = 93.33
c = 75.553	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 2.1: 2025-04-23
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.