SAXSdb — 4i4h

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

Cytochrome P450 3A4

Homo sapiens

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 ;pyridin-3-ylmethyl [(2R,5S)-5-{[N-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-D-valyl]amino}-1,6-diphenylhexan-2-yl]carbamate ; × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	PROTOPORPHYRIN IX CONTAINING FE × 4 ;pyridin-3-ylmethyl [(2R,5S)-5-{[N-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-D-valyl]amino}-1,6-diphenylhexan-2-yl]carbamate ; × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CP3A4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–483； UniProt 1–503

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	4i4h
Deposition date deposition_date	2012-11-27
Structure title title	Crystal structure of CYP3A4 ligated to pyridine-substituted desoxyritonavir
Keywords keywords	;monooxygenase, cytochrome P450 reductase, cytochrome b5, endoplasmic reticulum, cytochrome P450, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex ;; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
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.

4i4h__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4i4h__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4i4h__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	41.45 Å
Rg (electron density)	40.32 Å
Total Rg	40.80 Å
Atom count	15084
Residues	1828
Excluded volume	274250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4i4h__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4i4h__assembly_2__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	Cytochrome P450 3A4
Molecular weight formula_weight	55757.8 kDa
EC 编号 ec_number	1.14.13.-, 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97
Mutation mutation	residues 3-22 deleted
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	3771

MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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	1

Entity 3 Entity 3 non-polymer

Description description	;pyridin-3-ylmethyl [(2R,5S)-5-{[N-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-D-valyl]amino}-1,6-diphenylhexan-2-yl]carbamate ;
Molecular weight formula_weight	698.9 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4i4ha_
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	4i4hA00
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	77.760 Å
Unit-cell length b length_b	100.060 Å
Unit-cell length c length_c	131.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	65.700 Å
R factor r_factor	0.1980
R_work r_work	0.1946
R_free r_free	0.2691

Crystal structure of CYP3A4 ligated to pyridine-substituted desoxyritonavir

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

Cytochrome P450 3A4

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

4i4h__assembly_2__model_1

4i4h__assembly_2__model_1 | I(q)

4i4h__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of CYP3A4 ligated to pyridine-substituted desoxyritonavir

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

Cytochrome P450 3A4

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

4i4h__assembly_2__model_1

4i4h__assembly_2__model_1 | I(q)

4i4h__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)