SAXSdb — 5ncf

▼

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

Protein enabled homolog

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	;(1~{S},4~{S},7~{R},10~{R})-14-[(3~{S},6~{R},8~{a}~{S})-1'-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylidene-spiro[1,2,3,8~{a}-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-2-oxidanylidene-3,14-diazatricyclo[8.4.0.0^{3,7}]tetradec-8-ene-4-carboxylic acid ; × 1 SULFATE ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;(1~{S},4~{S},7~{R},10~{R})-14-[(3~{S},6~{R},8~{a}~{S})-1'-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylidene-spiro[1,2,3,8~{a}-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-2-oxidanylidene-3,14-diazatricyclo[8.4.0.0^{3,7}]tetradec-8-ene-4-carboxylic acid ; × 1 GLYCEROL × 3 NITRATE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENAH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–113； UniProt 1–111 Author chain B； PDBConstruct 3–113； UniProt 1–111

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	5ncf
Deposition date deposition_date	2017-03-04
Structure title title	ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-4]-OH
Keywords keywords	proline-rich motif, Ena/VASP inhibitor, actin, protein-protein interaction, cell adhesion; CELL ADHESION
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.

5ncf__assembly_1__model_1

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

Download this curve (.dat)

5ncf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ncf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.08 Å
Rg (electron density)	13.73 Å
Total Rg	14.99 Å
Atom count	1841
Residues	113
Excluded volume	16573 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ncf__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ncf__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	Protein enabled homolog
Molecular weight formula_weight	12628.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4029

GSMSEQSICQARAAVMVYDDANKKWVPAGGSTGFSRVHIYHHTGNNTFRVVGRKIQDHQVVINCAIPKGLKYNQATQTFHQWRDARQVYGLNFGSKEDANVFASAMMHALEVL

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	;(1~{S},4~{S},7~{R},10~{R})-14-[(3~{S},6~{R},8~{a}~{S})-1'-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylidene-spiro[1,2,3,8~{a}-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-2-oxidanylidene-3,14-diazatricyclo[8.4.0.0^{3,7}]tetradec-8-ene-4-carboxylic acid ;
Molecular weight formula_weight	692.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

▼

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5ncfa1
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.4 — Enabled/VASP homology 1 domain (EVH1 domain)

Domain ID domain_id	d5ncfa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5ncfb_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.4 — Enabled/VASP homology 1 domain (EVH1 domain)

CATH v4.4 (2 domains)

Domain ID domain_id	5ncfA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	5ncfB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

▶

Unit-cell length a length_a	34.715 Å
Unit-cell length b length_b	43.364 Å
Unit-cell length c length_c	44.181 Å
Unit-cell angle α angle_alpha	60.97 °
Unit-cell angle β angle_beta	84.19 °
Unit-cell angle γ angle_gamma	84.16 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	38.560 Å
R factor r_factor	0.2753
R_work r_work	0.2188
R_free r_free	0.2575

ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-4]-OH

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

Protein enabled homolog

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

5ncf__assembly_1__model_1

5ncf__assembly_1__model_1 | I(q)

5ncf__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-4]-OH

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

Protein enabled homolog

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

5ncf__assembly_1__model_1

5ncf__assembly_1__model_1 | I(q)

5ncf__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)