SAXSdb — 3cy1

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

Cytochrome P450 121

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 6 PROTOPORPHYRIN IX CONTAINING FE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CP121_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–396； UniProt 1–396

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3cy1
Deposition date deposition_date	2008-04-25
Structure title title	Crystal structure of the cytochrome P450 CYP121 S279A mutant from M. tuberculosis
Keywords keywords	cytochrome P450, CYP121, mycobacterium tuberculosis, Heme, Iron, Metal-binding, Monooxygenase, Oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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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.

3cy1__assembly_1__model_1

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

Download this curve (.dat)

3cy1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cy1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.97 Å
Rg (electron density)	27.93 Å
Total Rg	28.72 Å
Atom count	6048
Residues	790
Excluded volume	108340 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cy1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cytochrome P450 121
Molecular weight formula_weight	43289.9 kDa
EC 编号 ec_number	1.14.-.-
Mutation mutation	S279A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3553

MTATVLLEVPFSARGDRIPDAVAELRTREPIRKVRTITGAEAWLVSSYALCTQVLEDRRFSMKETAAAGAPRLNALTVPPEVVNNMGNIADAGLRKAVMKAITPKAPGLEQFLRDTANSLLDNLITEGAPADLRNDFADPLATALHCKVLGIPQEDGPKLFRSLSIAFMSSADPIPAAKINWDRDIEYMAGILENPNITTGLMGELSRLRKDPAYSHVSDELFATIGVTFFGAGVISTGSFLTTALISLIQRPQLRNLLHEKPELIPAGVEELLRINLAFADGLPRLATADIQVGDVLVRKGELVLVLLEGANFDPEHFPNPGSIELDRPNPTSHLAFGRGQHFCPGSALGRRHAQIGIEALLKKMPGVDLAVPIDQLVWRTRFQRRIPERLPVLW

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	415

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3cy1a_
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.104.1.1 — Cytochrome P450

CATH v4.4 (1 domains)

Domain ID domain_id	3cy1A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

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Unit-cell length a length_a	77.670 Å
Unit-cell length b length_b	77.670 Å
Unit-cell length c length_c	263.503 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	30.020 Å
R factor r_factor	0.1859
R_work r_work	0.1846
R_free r_free	0.2110

Crystal structure of the cytochrome P450 CYP121 S279A mutant from M. tuberculosis

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

Cytochrome P450 121

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

3cy1__assembly_1__model_1

3cy1__assembly_1__model_1 | I(q)

3cy1__assembly_1__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the cytochrome P450 CYP121 S279A mutant from M. tuberculosis

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

Cytochrome P450 121

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

3cy1__assembly_1__model_1

3cy1__assembly_1__model_1 | I(q)

3cy1__assembly_1__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)