SAXSdb — 1c6v

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

PROTEIN (SIV INTEGRASE)

Simian immunodeficiency virus

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 813–976 Chain B； UniProt 813–976 Chain C； UniProt 813–976 Chain D； UniProt 813–976	Fragment：RESIDUES 813-976 Mutation：F185H	PROTEIN (SIU89134) × 1 （Q87706）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.7；0.1 M MES, PH=5.7, PEG6K 8%, 15% DIOXANE	Resolution 3.00 Å R-free 0.362

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 1C6V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2SAM STRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COMPLEX WITH AN IRREVERSIBLE NON-PEPTIDE INHIBITOR Deposited 1994-07-08	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 106–203（98 aa）	Not recorded	EPN 3-(4-NITRO-PHENOXY)-PROPAN-1-OL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q88016_SIVCZ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–164； UniProt 813–976 Author chain B； PDBConstruct 1–164； UniProt 813–976 Author chain C； PDBConstruct 1–164； UniProt 813–976 Author chain D； PDBConstruct 1–164； UniProt 813–976

PROTEIN (SIU89134)

Simian immunodeficiency virus

UniProt Q87706

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain X； UniProt 979–1059	Fragment：RESIDUES 979-1059	PROTEIN (SIV INTEGRASE) × 4 （Q88016）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.7；0.1 M MES, PH=5.7, PEG6K 8%, 15% DIOXANE	Resolution 3.00 Å R-free 0.362

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 1C6V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SIP ALTERNATIVE NATIVE FLAP CONFORMATION REVEALED BY 2.3 ANGSTROMS RESOLUTION STRUCTURE OF SIV PROTEINASE Deposited 1994-04-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 106–203（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q87706_SIVCZ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain X； PDBConstruct 1–81； UniProt 979–1059

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	1c6v
Deposition date deposition_date	1999-12-21
Structure title title	SIV INTEGRASE (CATALYTIC DOMAIN + DNA BIDING DOMAIN COMPRISING RESIDUES 50-293) MUTANT WITH PHE 185 REPLACED BY HIS (F185H)
Keywords keywords	DNA INTEGRATION, DNA BINDING PROTEIN; DNA BINDING 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	30.05 Å
Radius of gyration Rg (electron density) rg_electron	29.38 Å
Forward intensity I(0) i0	84275000.00
Molecular weight molecular_weight	70704.0 kDa
Excluded volume excluded_volume	88035 Å³
Envelope volume envelope_volume	113820 Å³
Hydration-shell volume shell_volume	32895 Å³
Envelope diameter envelope_diameter	96.0 Å
Shell Rg shell_rg	36.01 Å
Envelope Rg envelope_rg	29.04 Å
Shape Rg shape_rg	29.37 Å
Total Rg total_rg	30.06 Å
Total atoms total_atoms	4964
Residues n_residues	630
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	95.9 Å
Rg (real space) rg_real	30.10 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	8.4270e+07
I(0) uncertainty (real space) i0_real_error	1.1470e+06
Rg (reciprocal space) rg_reciprocal	30.08 Å
I(0) (reciprocal space) i0_reciprocal	84270000.0000
Solution quality estimate total_estimate	0.8809
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.8 Å
Skewness Skewness skewness	0.358
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20700000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.798

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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	PROTEIN (SIV INTEGRASE)
Molecular weight formula_weight	18406.0 kDa
Mutation mutation	F185H
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	5030

IHGQVNSDLGTWQMDCTHLEGKIVIVAVHVASGFIEAEVIPQETGRQTALFLLKLAGRWPITHLHTDNGANFASQEVKMVAWWAGIEHTFGVPYNPQSQGVVEAMNHHLKNQIDRIREQANSVETIVLMAVHCMNHKRRGGIGDMTPAERLINMITTEQEIQFQ

来源 Source

来源生物 organism	Simian immunodeficiency virus
NCBI Class编号 ncbi_taxonomy_id	11723
宿主生物 host_organism	Escherichia coli K12

Entity 2 Entity 2 polymer

Description description	PROTEIN (SIU89134)
Molecular weight formula_weight	9185.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

QQSKNSKFKNFRVYYREGRDQLWKGPGELLWKGEGAVLLKVGTDIKVVPRRKAKIIKDYGGGKEVDSSSHMEDTGEAREVA

来源 Source

来源生物 organism	Simian immunodeficiency virus
NCBI Class编号 ncbi_taxonomy_id	11723
宿主生物 host_organism	Escherichia coli K12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1c6va_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.2 — Retroviral integrase, catalytic domain

Domain ID domain_id	d1c6vb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.2 — Retroviral integrase, catalytic domain

Domain ID domain_id	d1c6vc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.2 — Retroviral integrase, catalytic domain

Domain ID domain_id	d1c6vd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.2 — Retroviral integrase, catalytic domain

Domain ID domain_id	d1c6vx_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.7 — DNA-binding domain of retroviral integrase
Family Family family	b.34.7.1 — DNA-binding domain of retroviral integrase

CATH v4.4 (5 domains)

Domain ID domain_id	1c6vA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	1c6vB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	1c6vC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	1c6vD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	1c6vX00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	10 — Integrase, C-terminal domain superfamily, retroviral

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8. Citations (1)

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Unit-cell length a length_a	79.570 Å
Unit-cell length b length_b	100.000 Å
Unit-cell length c length_c	150.500 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.3620

fit	/app/data/saxs_computation/c6/1c6v/1c6v.fit
pddf	/app/data/pr_computation/c6/1c6v/1c6v.pr.out
profile	/app/data/saxs_computation/c6/1c6v/1c6v.dat

SIV INTEGRASE (CATALYTIC DOMAIN + DNA BIDING DOMAIN COMPRISING RESIDUES 50-293) MUTANT WITH PHE 185 REPLACED BY HIS (F185H)

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

PROTEIN (SIV INTEGRASE)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (SIU89134)

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)