4ny0

Crystal structure of FERM domain of human focal adhesion kinase

Method: X-RAY DIFFRACTION Dmax: 146.1 Å Quality: GOOD

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

Focal adhesion kinase 1

Homo sapiens

UniProt Q05397

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 31–405 Chain D; UniProt 31–405 Fragment:FERM domain, UNP RESIDUES 31-405 Mutation:F85L, W181G No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293.15 K;17% PEG 10000, 0.1M Ammonium Sulfate, 0.1M bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K Resolution 2.80 Å R-free 0.230
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 31–405 Chain C; UniProt 31–405 Fragment:FERM domain, UNP RESIDUES 31-405 Mutation:F85L, W181G No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293.15 K;17% PEG 10000, 0.1M Ammonium Sulfate, 0.1M bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K Resolution 2.80 Å R-free 0.230

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

38 other PDB entries and 80 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FAK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–376; UniProt 31–405 Author chain B; PDBConstruct 2–376; UniProt 31–405 Author chain C; PDBConstruct 2–376; UniProt 31–405 Author chain D; PDBConstruct 2–376; UniProt 31–405

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4ny0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ny0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ny0
Deposition date deposition_date2013-12-10
Structure title titleCrystal structure of FERM domain of human focal adhesion kinase
Keywords keywordsFERM domain, focal adhesion kinase, focal targeting domain, integrin signaling, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier46.76
Radius of gyration Rg (electron density) rg_electron46.67
Forward intensity I(0) i0328600000.00
Molecular weight molecular_weight152090.0 kDa
Excluded volume excluded_volume191500 ų
Envelope volume envelope_volume285890 ų
Hydration-shell volume shell_volume52528 ų
Envelope diameter envelope_diameter149.4
Shell Rg shell_rg49.23
Envelope Rg envelope_rg45.60
Shape Rg shape_rg46.65
Total Rg total_rg46.86
Total atoms total_atoms10722
Residues n_residues1322
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax146.1
Rg (real space) rg_real46.91
Rg uncertainty (real space) rg_real_error1.38
I(0) (real space) i0_real3.2860e+08
I(0) uncertainty (real space) i0_real_error6.5440e+06
Rg (reciprocal space) rg_reciprocal46.76
I(0) (reciprocal space) i0_reciprocal328500000.0000
Solution quality estimate total_estimate0.8473
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.0
Skewness Skewness skewness0.239
Kurtosis Kurtosis kurtosis-0.852
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22050000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.315

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd4ny0a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd4ny0a2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd4ny0a3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd4ny0b1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd4ny0b2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd4ny0b3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd4ny0d1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd4ny0d2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd4ny0d3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id4ny0A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4ny0A02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id4ny0A03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id4ny0B01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4ny0B02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id4ny0B03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id4ny0C01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4ny0C02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id4ny0C03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id4ny0D01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4ny0D02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id4ny0D03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

8. Citations (1)

9. Files and Curves (10)