4B7D | pdb_00004b7d

PikC bound to the 10-DML analog with the 3-(N,N-dimethylamino) propanoate anchoring group

PDB DOI: https://doi.org/10.2210/pdb4B7D/pdb

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

Deposited: 2012-08-17 Released: 2013-08-28
Deposition Author(s): Podust, L.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.257 (Depositor), 0.253 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Recognition of Synthetic Substrates by P450 Pikc

Podust, L.M.

To be published.

Macromolecule Content

Total Structure Weight: 98.84 kDa
Atom Count: 6,719
Modeled Residue Count: 786
Deposited Residue Count: 872
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 HYDROXYLASE PIKC	A, B	436	Streptomyces venezuelae	Mutation(s): 0 EC: 1.14.15.33
UniProt
Find proteins for O87605 (Streptomyces venezuelae) Explore O87605 Go to UniProtKB: O87605
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O87605
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
QLE Query on QLE Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	[(3R,4S,5S,7R,9E,11R,12R)-12-ethyl-3,5,7,11-tetramethyl-2,8-bis(oxidanylidene)-1-oxacyclododec-9-en-4-yl] 3-(dimethylamino)propanoate C₂₂ H₃₇ N O₅ ARTBSYNHBBHIBV-HSYQSNAQSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.257 (Depositor), 0.253 (DCC)
R-Value Work: 0.200 (Depositor), 0.199 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.766	α = 79.96
b = 58.042	β = 79.52
c = 96.415	γ = 88.73

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-08-28

Deposition Author(s):

Podust, L.M.

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release
Version 1.1: 2013-12-04
Changes: Non-polymer description
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description