4BF4 | pdb_00004bf4

PikC D50N mutant in complex with the engineered cycloalkane substrate mimic bearing a termianl N,N-dimethylamino group

PDB DOI: https://doi.org/10.2210/pdb4BF4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces venezuelae
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2013-03-14 Released: 2014-03-26
Deposition Author(s): Podust, L.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.279 (Depositor), 0.277 (DCC)
R-Value Work:
0.196 (Depositor), 0.199 (DCC)
R-Value Observed:
0.200 (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

Recognition of Synthetic Substrates by P450 Pikc

Podust, L.M.

To be published.

Macromolecule Content

Total Structure Weight: 783.9 kDa
Atom Count: 50,342
Modeled Residue Count: 6,345
Deposited Residue Count: 6,976
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, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	436	Streptomyces venezuelae	Mutation(s): 1 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 AA [auth F] SDF format, chain CA [auth G] SDF format, chain EA [auth H] SDF format, chain HA [auth I] SDF format, chain KA [auth J] SDF format, chain MA [auth K] SDF format, chain NA [auth L] SDF format, chain OA [auth M] SDF format, chain PA [auth N] SDF format, chain Q [auth A] SDF format, chain QA [auth O] SDF format, chain S [auth B] SDF format, chain TA [auth P] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain KA [auth J] MOL2 format, chain MA [auth K] MOL2 format, chain NA [auth L] MOL2 format, chain OA [auth M] MOL2 format, chain PA [auth N] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth O] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth P] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain KA [auth J] mmCIF format, chain MA [auth K] mmCIF format, chain NA [auth L] mmCIF format, chain OA [auth M] mmCIF format, chain PA [auth N] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth O] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth P] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	AA [auth F] CA [auth G] EA [auth H] HA [auth I] KA [auth J] AA [auth F], CA [auth G], EA [auth H], HA [auth I], KA [auth J], MA [auth K], NA [auth L], OA [auth M], PA [auth N], Q [auth A], QA [auth O], S [auth B], TA [auth P], V [auth C], X [auth D], Z [auth E]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain HA [auth I] Focus chain KA [auth J] Focus chain MA [auth K] Focus chain NA [auth L] Focus chain OA [auth M] Focus chain PA [auth N] Focus chain Q [auth A] Focus chain QA [auth O] Focus chain S [auth B] Focus chain TA [auth P] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain HA [auth I] Focus chain KA [auth J] Focus chain MA [auth K] Focus chain NA [auth L] Focus chain OA [auth M] Focus chain PA [auth N] Focus chain Q [auth A] Focus chain QA [auth O] Focus chain S [auth B] Focus chain TA [auth P] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]
17Q Query on 17Q Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain DA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain DA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain DA [auth G]	DA [auth G], W [auth C]	1.7.6 5-cyclododecyloxy-N,N-dimethyl-pentan-1-amine C₁₉ H₃₉ N O IWMFMRACOCTPPO-UHFFFAOYSA-N		Interactions Focus chain DA [auth G] Focus chain W [auth C] Interactions & Density Focus chain DA [auth G] Focus chain W [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain FA [auth H] SDF format, chain GA [auth H] SDF format, chain IA [auth I] SDF format, chain JA [auth I] SDF format, chain LA [auth J] SDF format, chain RA [auth O] SDF format, chain SA [auth O] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth D] SDF format, chain R [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain RA [auth O] MOL2 format, chain SA [auth O] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain R [auth A] mmCIF format, chain BA [auth F] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain IA [auth I] mmCIF format, chain JA [auth I] mmCIF format, chain LA [auth J] mmCIF format, chain RA [auth O] mmCIF format, chain SA [auth O] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain R [auth A]	BA [auth F] FA [auth H] GA [auth H] IA [auth I] JA [auth I] BA [auth F], FA [auth H], GA [auth H], IA [auth I], JA [auth I], LA [auth J], R [auth A], RA [auth O], SA [auth O], T [auth B], U [auth B], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth F] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain LA [auth J] Focus chain R [auth A] Focus chain RA [auth O] Focus chain SA [auth O] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain LA [auth J] Focus chain R [auth A] Focus chain RA [auth O] Focus chain SA [auth O] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.279 (Depositor), 0.277 (DCC)
R-Value Work: 0.196 (Depositor), 0.199 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.273	α = 66.48
b = 130.113	β = 70.25
c = 134.898	γ = 72.23

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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Podust, L.M.

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description