SAXSdb — 4bik

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

INTERMEDILYSIN

STREPTOCOCCUS INTERMEDIUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CD59 GLYCOPROTEIN × 1 （P13987）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CD59 GLYCOPROTEIN × 1 （P13987）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LCB8_STRIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 37–535； UniProt 34–532 Author chain C； PDBConstruct 37–535； UniProt 34–532

CD59 GLYCOPROTEIN

HOMO SAPIENS

UniProt P13987

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	INTERMEDILYSIN × 1 （Q9LCB8）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	INTERMEDILYSIN × 1 （Q9LCB8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD59_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–78； UniProt 26–102 Author chain D； PDBConstruct 2–78； UniProt 26–102

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	4bik
Deposition date deposition_date	2013-04-10
Structure title title	Structure of a disulfide locked mutant of Intermedilysin with human CD59
Keywords keywords	COMPLEMENT, CHOLESTEROL DEPENDENT CYTOTOXIN, IMMUNE SYSTEM, MEMBRANE ATTACK COMPLEX; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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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.

4bik__assembly_1__model_1

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

Download this curve (.dat)

4bik__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bik__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.51 Å
Rg (electron density)	34.56 Å
Total Rg	34.70 Å
Atom count	4189
Residues	533
Excluded volume	74197 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bik__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4bik__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	INTERMEDILYSIN
Molecular weight formula_weight	59056.9 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8387

MGGSHHHHHHGMASMTGGQQMGRDLYDDDDKDRWGSETPTKPKAAQTEKKTEKKPENSNSEAAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVIEKKKQSISNATSKLSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENPSNSTVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVDFSSVHKGEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSNVSYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKICAVVLGGNPGEASKVCTGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSYKDGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVRNIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVKDNTD

Source Source

Source organism organism	STREPTOCOCCUS INTERMEDIUS
NCBI taxonomy ID ncbi_taxonomy_id	1338
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	CD59 GLYCOPROTEIN
Molecular weight formula_weight	9204.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENELTYYCCKKDLCNFNEQLENC

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 K-12

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	4bikA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	4bikA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4bikA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	4bikA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

Domain ID domain_id	4bikB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	4bikC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	4bikC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4bikC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	4bikC04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

Domain ID domain_id	4bikD00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

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Unit-cell length a length_a	27.400 Å
Unit-cell length b length_b	101.450 Å
Unit-cell length c length_c	112.880 Å
Unit-cell angle α angle_alpha	63.75 °
Unit-cell angle β angle_beta	89.95 °
Unit-cell angle γ angle_gamma	90.02 °
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	3.494 Å
Low-resolution limit resolution_low	45.494 Å
R factor r_factor	0.2032
R_work r_work	0.2118
R_free r_free	0.2661

Structure of a disulfide locked mutant of Intermedilysin with human CD59

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

INTERMEDILYSIN

State in the Current Structure

Other States of the Same Protein in the Database

CD59 GLYCOPROTEIN

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

4bik__assembly_1__model_1

4bik__assembly_1__model_1 | I(q)

4bik__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Structure of a disulfide locked mutant of Intermedilysin with human CD59

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

INTERMEDILYSIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CD59 GLYCOPROTEIN

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

4bik__assembly_1__model_1

4bik__assembly_1__model_1 | I(q)

4bik__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)