4bf4

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

Method: X-RAY DIFFRACTION

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOCHROME P450 HYDROXYLASE PIKC

STREPTOMYCES VENEZUELAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 1 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count
13	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count
14	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count
15	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 2 water × 1	Consistent with protein count
16	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 1.7.6 5-cyclododecyloxy-N,N-dimethyl-pentan-1-amine × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 1.7.6 5-cyclododecyloxy-N,N-dimethyl-pentan-1-amine × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 2 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O87605_STRVZ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–436； UniProt 1–416 Author chain B； PDBConstruct 21–436； UniProt 1–416 Author chain C； PDBConstruct 21–436； UniProt 1–416 Author chain D； PDBConstruct 21–436； UniProt 1–416 Author chain E； PDBConstruct 21–436； UniProt 1–416 Author chain F； PDBConstruct 21–436； UniProt 1–416 Author chain G； PDBConstruct 21–436； UniProt 1–416 Author chain H； PDBConstruct 21–436； UniProt 1–416 Author chain I； PDBConstruct 21–436； UniProt 1–416 Author chain J； PDBConstruct 21–436； UniProt 1–416 Author chain K； PDBConstruct 21–436； UniProt 1–416 Author chain L； PDBConstruct 21–436； UniProt 1–416 Author chain M； PDBConstruct 21–436； UniProt 1–416 Author chain N； PDBConstruct 21–436； UniProt 1–416 Author chain O； PDBConstruct 21–436； UniProt 1–416 Author chain P； PDBConstruct 21–436； UniProt 1–416

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4bf4
Deposition date deposition_date	2013-03-14
Structure title title	PikC D50N mutant in complex with the engineered cycloalkane substrate mimic bearing a termianl N,N-dimethylamino group
Keywords keywords	OXIDOREDUCTASE, MONOOXYGENASE, PIKROMYCIN BIOSYNTHESIS; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4bf4__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4bf4__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bf4__assembly_6__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.03 Å
Rg (electron density)	20.66 Å
Total Rg	21.54 Å
Atom count	3089
Residues	396
Excluded volume	54817 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bf4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4bf4__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4bf4__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4bf4__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4bf4__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4bf4__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4bf4__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`4bf4__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`4bf4__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`4bf4__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`4bf4__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`4bf4__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`4bf4__assembly_13__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`4bf4__assembly_14__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
15	1	`4bf4__assembly_15__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
16	1	`4bf4__assembly_16__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	CYTOCHROME P450 HYDROXYLASE PIKC
Molecular weight formula_weight	48267.8 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	50342

MGSSHHHHHHSSGLVPRGSHMRRTQQGTTASPPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGNEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRRGREAGRRTG

Source Source

Source organism organism	STREPTOMYCES VENEZUELAE
NCBI taxonomy ID ncbi_taxonomy_id	54571
Host organism host_organism	ESCHERICHIA COLI K-12

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	1.7.6 5-cyclododecyloxy-N,N-dimethyl-pentan-1-amine
Molecular weight formula_weight	297.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	514

▼

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d4bf4a_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4b_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4c_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4d_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4e_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4f_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4g_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4h_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4i_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4j_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4k_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4l_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4m_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4n_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4o_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d4bf4p_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

CATH v4.4 (16 domains)

Domain ID domain_id	4bf4A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4E00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4G00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4H00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4I00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4J00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4K00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4L00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4M00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4N00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4O00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	4bf4P00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

▶

Unit-cell length a length_a	110.273 Å
Unit-cell length b length_b	130.113 Å
Unit-cell length c length_c	134.898 Å
Unit-cell angle α angle_alpha	66.48 °
Unit-cell angle β angle_beta	70.25 °
Unit-cell angle γ angle_gamma	72.23 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	119.840 Å
R factor r_factor	0.2001
R_work r_work	0.1959
R_free r_free	0.2790

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOCHROME P450 HYDROXYLASE PIKC

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4bf4__assembly_6__model_1

4bf4__assembly_6__model_1 | I(q)

4bf4__assembly_6__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOCHROME P450 HYDROXYLASE PIKC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4bf4__assembly_6__model_1

4bf4__assembly_6__model_1 | I(q)

4bf4__assembly_6__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)