SAXSdb — 4k2p

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

T-lymphoma invasion and metastasis-inducing protein 1

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 429–702	Fragment：PH-CC-Ex domain (UNP residues 429-702) Mutation：K596A, K597A, K598A, M580L, M586L	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M lithium sulfate, 0.1 M Tris, 19% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.98 Å R-free 0.236
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 429–702	Fragment：PH-CC-Ex domain (UNP residues 429-702) Mutation：K596A, K597A, K598A, M580L, M586L	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M lithium sulfate, 0.1 M Tris, 19% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.98 Å R-free 0.236
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 429–702	Fragment：PH-CC-Ex domain (UNP residues 429-702) Mutation：K596A, K597A, K598A, M580L, M586L	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M lithium sulfate, 0.1 M Tris, 19% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.98 Å R-free 0.236
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 429–702	Fragment：PH-CC-Ex domain (UNP residues 429-702) Mutation：K596A, K597A, K598A, M580L, M586L	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M lithium sulfate, 0.1 M Tris, 19% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.98 Å R-free 0.236

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.

Other PDB	Difference from Current Entry 4K2P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3KZD Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Deposited 2009-12-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 841–930（90 aa） Fragment：PDZ Domain	Mutation：Q844H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；288 K；20% (w/v) PEG 3350, 0.2 M NaSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.30 Å R-free 0.224
3KZE Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in Complex With SSRKEYYA Peptide Deposited 2009-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 841–930（90 aa） Fragment：PDZ Domain Chain B 841–930（90 aa） Fragment：PDZ Domain Chain C 841–930（90 aa） Fragment：PDZ Domain	Mutation：Q844H Mutation：Q844H Mutation：Q844H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；288 K；20% (w/v) PEG 3350, 0.2 M Na2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.80 Å R-free 0.212
4GVC Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with phosphorylated Syndecan1 Peptide Deposited 2012-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 841–930（90 aa） Fragment：PDZ domain (UNP residues 841-930)	Not recorded	CL CHLORIDE ION × 2 ANS 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID) × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1 M sodium acetate, 25% PEG4000, 8% isopropanol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.54 Å R-free 0.200
4GVD Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with Syndecan1 Peptide Deposited 2012-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 841–930（90 aa） Fragment：PDZ domain (UNP residues 841-930)	Not recorded	CL CHLORIDE ION × 2 NA SODIUM ION × 1 ANS 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1 M MES, 20% PEG8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.243
4GVD Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with Syndecan1 Peptide Deposited 2012-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 841–930（90 aa） Fragment：PDZ domain (UNP residues 841-930)	Not recorded	CL CHLORIDE ION × 1 NA SODIUM ION × 1 ANS 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1 M MES, 20% PEG8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.243
4K2O The Structure of a Triple Mutant of the Tiam1 PH-CC-Ex Domain Deposited 2013-04-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 429–702（274 aa） Fragment：PH-CC-Ex domain (UNP residues 429-702)	Mutation：K596A, K597A, K598A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M calcium chloride, 0.1 M Tris, 20% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.15 Å R-free 0.220
4NXP Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) Deposited 2013-12-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 841–930（90 aa） Fragment：PDZ domain	Mutation：L911M, K912E, L915F, L920V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；1.5M Ammonium Sulfate, 0.1M Tris, pH=8.5, 12% Glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.258
4NXQ Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Caspr4 Peptide Deposited 2013-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 841–930（90 aa） Fragment：PDZ domain	Mutation：L911M, K912E, L915F, L920V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1M Magnesium chloride, 0.1M MES, pH=6.5, 20% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.236
4NXQ Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Caspr4 Peptide Deposited 2013-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 841–930（90 aa） Fragment：PDZ domain	Mutation：L911M, K912E, L915F, L920V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1M Magnesium chloride, 0.1M MES, pH=6.5, 20% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.236
4NXQ Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Caspr4 Peptide Deposited 2013-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 841–930（90 aa） Fragment：PDZ domain	Mutation：L911M, K912E, L915F, L920V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1M Magnesium chloride, 0.1M MES, pH=6.5, 20% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.236
4NXR Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Neurexin-1 Peptide Deposited 2013-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 841–930（90 aa） Fragment：PDZ domain	Mutation：L911M, K912E, L915F, L920V	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ANS 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；0.1M Sodium acetate, 0.1M HEPES, pH=7.5, 22% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.195

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TIAM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–276； UniProt 429–702 Author chain B； PDBConstruct 3–276； UniProt 429–702 Author chain C； PDBConstruct 3–276； UniProt 429–702 Author chain D； PDBConstruct 3–276； UniProt 429–702

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	4k2p
Deposition date deposition_date	2013-04-09
Structure title title	The Structure of a Quintuple Mutant of the Tiam1 PH-CC-Ex Domain
Keywords keywords	PH and coiled coil domain, phosphoinositide binding; protein-protein interaction, Par-3, tight junctions, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	34.56 Å
Radius of gyration Rg (electron density) rg_electron	33.98 Å
Forward intensity I(0) i0	169228000.00
Molecular weight molecular_weight	105950.0 kDa
Excluded volume excluded_volume	133840 Å³
Envelope volume envelope_volume	193330 Å³
Hydration-shell volume shell_volume	47823 Å³
Envelope diameter envelope_diameter	123.8 Å
Shell Rg shell_rg	40.64 Å
Envelope Rg envelope_rg	33.09 Å
Shape Rg shape_rg	33.92 Å
Total Rg total_rg	34.74 Å
Total atoms total_atoms	14984
Residues n_residues	941
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	114.8 Å
Rg (real space) rg_real	34.44 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	1.6920e+08
I(0) uncertainty (real space) i0_real_error	2.8350e+06
Rg (reciprocal space) rg_reciprocal	34.52 Å
I(0) (reciprocal space) i0_reciprocal	169200000.0000
Solution quality estimate total_estimate	0.8667
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.4 Å
Skewness Skewness skewness	0.220
Kurtosis Kurtosis kurtosis	-0.168
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17760000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.893

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	T-lymphoma invasion and metastasis-inducing protein 1
Molecular weight formula_weight	31163.9 kDa
Mutation mutation	K596A, K597A, K598A, M580L, M586L
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15771

GSAAQGTVRKAGALAVKNFLVHKKNKKVESATRRKWKHYWVSLKGCTLFFYESDGRSGIDHNSIPKHAVWVENSIVQAVPEHPKKDFVFCLSNSLGDAFLFQTTSQTELENWITAIHSACATAVARHHHKEDTLRLLKSEIKKLEQKIDMDEKLKKMGELQLSSVTDSKAAATILDQIFVWEQNLEQFQMDLFRFRCYLASLQGGELPNPKRLLAFASRPTKVAMGRLGIFSVSSFHALVAARTGETGVRRRTQAMSRSASKRRSRFSSLWGLDTT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	749

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4k2pA01
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	4k2pA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4k2pB01
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	4k2pB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4k2pC01
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	4k2pC02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4k2pD01
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	4k2pD02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	680 —

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8. Citations (1)

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Unit-cell length a length_a	80.507 Å
Unit-cell length b length_b	70.111 Å
Unit-cell length c length_c	87.753 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.19 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	19.703 Å
R factor r_factor	0.1938
R_work r_work	0.1917
R_free r_free	0.2359

fit	/app/data/saxs_computation/k2/4k2p/4k2p.fit
pddf	/app/data/pr_computation/k2/4k2p/4k2p.pr.out
profile	/app/data/saxs_computation/k2/4k2p/4k2p.dat

The Structure of a Quintuple Mutant of the Tiam1 PH-CC-Ex Domain

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

T-lymphoma invasion and metastasis-inducing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction