SAXSdb — 1ea6

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

PMS1 PROTEIN HOMOLOG 2

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 1–364	Fragment：N-TERMINAL 40KDA, RESIDUES 1-364	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.2；2-2.4 M NA/K PHOSPHATE (PH 6.2) 0.2 M LICL	Resolution 2.70 Å R-free 0.262
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–364	Fragment：N-TERMINAL 40KDA, RESIDUES 1-364	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.2；2-2.4 M NA/K PHOSPHATE (PH 6.2) 0.2 M LICL	Resolution 2.70 Å R-free 0.262

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 1EA6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H7S N-terminal 40kDa fragment of human PMS2 Deposited 2001-07-10	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–365（365 aa） Fragment：N-TERMINAL 40 KDA FRAGMENT	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH 6.2) 0.2 M LICL	Resolution 1.95 Å R-free 0.243
1H7S N-terminal 40kDa fragment of human PMS2 Deposited 2001-07-10	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–365（365 aa） Fragment：N-TERMINAL 40 KDA FRAGMENT	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH 6.2) 0.2 M LICL	Resolution 1.95 Å R-free 0.243
1H7U hPMS2-ATPgS Deposited 2001-07-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–365（365 aa） Fragment：GHL ATPASE, RESIDUES 1-365	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH=6.2) 0.2 M LICL, pH 6.20	Resolution 2.70 Å R-free 0.270
1H7U hPMS2-ATPgS Deposited 2001-07-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–365（365 aa） Fragment：GHL ATPASE, RESIDUES 1-365	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH=6.2) 0.2 M LICL, pH 6.20	Resolution 2.70 Å R-free 0.270
5U5R Crystal Structure and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a PMS2 NLS Peptide Deposited 2016-12-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 573–583（11 aa）	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.600-0.625 M sodium citrate (pH 6) and 10 mM DTT	Resolution 2.10 Å R-free 0.207
6MFQ Crystal structure of a PMS2 variant Deposited 2018-09-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–365（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289.15 K；Crystals were obtained in conditions containing 4% tacsimate pH 5 (v/v) and 25% PEG 3350 (w/v). The concentrated PMS2 G207E protein (7 mg/mL) was combined with 0.1ul of an additive (0.1 M calcium chloride dehydrate) prior to the addition of crystallization reagent in a 1:1 ratio.	Resolution 2.60 Å R-free 0.232
6MFQ Crystal structure of a PMS2 variant Deposited 2018-09-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–365（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289.15 K；Crystals were obtained in conditions containing 4% tacsimate pH 5 (v/v) and 25% PEG 3350 (w/v). The concentrated PMS2 G207E protein (7 mg/mL) was combined with 0.1ul of an additive (0.1 M calcium chloride dehydrate) prior to the addition of crystallization reagent in a 1:1 ratio.	Resolution 2.60 Å R-free 0.232
7RCB Crystal Structure of a PMS2 VUS Deposited 2021-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–365（365 aa） Chain B 1–365（365 aa）	Mutation：N335S Mutation：N335S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；289.15 K；1:1 7.5 mg/mL protein with 8% v/v Tacsimate, pH 5.8, 25% w/v PEG3350	Resolution 2.00 Å R-free 0.198
7RCI Crystal Structure of a PMS2 VUS with Substrate Deposited 2021-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–365（365 aa） Chain B 1–365（365 aa）	Mutation：N335S Mutation：N335S	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；289.15 K；1:1 7.5 mg/mL protein with 8% v/v Tacsimate, pH 5.8, 25% w/v PEG3350	Resolution 2.12 Å R-free 0.248
7RCK Crystal Structure of PMS2 with Substrate Deposited 2021-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–365（365 aa） Chain B 1–365（365 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；289.15 K；1:1 7.5 mg/mL protein with 8% v/v Tacsimate, pH 5.8, 25% w/v PEG3350	Resolution 2.04 Å R-free 0.234
9S89 N-terminal 40kDa fragment of human PMS2 with covalent ligand NP1867 Deposited 2025-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–365（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.229

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

View Construct and Data Evidence

UniProt name	PMS2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–364； UniProt 1–364 Author chain B； PDBConstruct 1–364； UniProt 1–364

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	1ea6
Deposition date deposition_date	2001-07-10
Structure title title	N-terminal 40kDa fragment of NhPMS2 complexed with ADP
Keywords keywords	DNA REPAIR, GHL ATPASE, HNPCC, MISMATCH REPAIR; DNA REPAIR
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	28.86 Å
Radius of gyration Rg (electron density) rg_electron	28.36 Å
Forward intensity I(0) i0	78319700.00
Molecular weight molecular_weight	68106.0 kDa
Excluded volume excluded_volume	84817 Å³
Envelope volume envelope_volume	108210 Å³
Hydration-shell volume shell_volume	32844 Å³
Envelope diameter envelope_diameter	111.6 Å
Shell Rg shell_rg	34.49 Å
Envelope Rg envelope_rg	28.60 Å
Shape Rg shape_rg	28.35 Å
Total Rg total_rg	29.00 Å
Total atoms total_atoms	4764
Residues n_residues	609
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	105.0 Å
Rg (real space) rg_real	28.92 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	7.8320e+07
I(0) uncertainty (real space) i0_real_error	1.3240e+06
Rg (reciprocal space) rg_reciprocal	28.89 Å
I(0) (reciprocal space) i0_reciprocal	78320000.0000
Solution quality estimate total_estimate	0.8359
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.3 Å
Skewness Skewness skewness	0.491
Kurtosis Kurtosis kurtosis	0.198
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18210000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.669; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PMS1 PROTEIN HOMOLOG 2
Molecular weight formula_weight	40426.2 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	4814

MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTRLMFDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQLGQGKRQPVVCTGGSPSIKENIGSVFGQKQLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAKVCRLVNEVYHMYNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLIGMFD

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ea6a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1ea6a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

Domain ID domain_id	d1ea6b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1ea6b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1ea6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	1ea6A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ea6B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	1ea6B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	75.043 Å
Unit-cell length b length_b	74.983 Å
Unit-cell length c length_c	135.294 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	24.690 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2620

fit	/app/data/saxs_computation/ea/1ea6/1ea6.fit
pddf	/app/data/pr_computation/ea/1ea6/1ea6.pr.out
profile	/app/data/saxs_computation/ea/1ea6/1ea6.dat

N-terminal 40kDa fragment of NhPMS2 complexed with ADP

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

PMS1 PROTEIN HOMOLOG 2

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