SAXSdb — 3mdb

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

Kinesin-like protein KIF13B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Arf-GAP with dual PH domain-containing protein 1 × 1 （O75689） UNKNOWN ATOM OR ION × 5 ZINC ION × 1 ;(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate ; × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Arf-GAP with dual PH domain-containing protein 1 × 1 （O75689） UNKNOWN ATOM OR ION × 6 ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KI13B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–124； UniProt 440–545 Author chain B； PDBConstruct 19–124； UniProt 440–545

Arf-GAP with dual PH domain-containing protein 1

Homo sapiens

UniProt O75689

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Kinesin-like protein KIF13B × 1 （Q9NQT8） UNKNOWN ATOM OR ION × 5 ZINC ION × 1 ;(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate ; × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Kinesin-like protein KIF13B × 1 （Q9NQT8） UNKNOWN ATOM OR ION × 6 ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ADAP1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 19–392； UniProt 1–374 Author chain D； PDBConstruct 19–392； UniProt 1–374

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	3mdb
Deposition date deposition_date	2010-03-30
Structure title title	Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4
Keywords keywords	;KINESIN, GAP, GTPASE ACTIVATION, STRUCTURAL GENOMICS CONSORTIUM, SGC, CYTOSKELETON, MICROTUBULE, MOTOR PROTEIN, ZINC-FINGER, TRANSPORT PROTEIN-HYDROLASE ACTIVATOR COMPLEX, ATP-binding, Nucleotide-binding, Phosphoprotein, Metal-binding, Nucleus ;; Transport Protein/Hydrolase Activator
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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3mdb__assembly_1__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`3mdb__assembly_2__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Kinesin-like protein KIF13B
Molecular weight formula_weight	13969.8 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	7107

MHHHHHHSSGRENLYFQGGIKVGDDKCFLVNLNADPALNELLVYYLKEHTLIGSANSQDIQLCGMGILPEHCIIDITSEGQVMLTPQKNTRTFVNGSSVSSPIQLHHGDRILWGNNHFFRLNLP

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

Entity 2 Entity 2 polymer

Description description	Arf-GAP with dual PH domain-containing protein 1
Molecular weight formula_weight	45695.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MHHHHHHSSGRENLYFQGMAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFIYPEKQEPYSAGYREGFLWKRGRDNGQFLSRKFVLTEREGALKYFNRNDAKEPKAVMKIEHLNATFQPAKIGHPHGLQVTYLKDNSTRNIFIYHEDGKEIVDWFNALRAARFHYLQVAFPGASDADLVPKLSRNYLKEGYMEKTGPKQTEGFRKRWFTMDDRRLMYFKDPLDAFARGEVFIGSKESGYTVLHGFPPSTQGHHWPHGITIVTPDRKFLFACETESDQREWVAAFQKAVDRPMLPQEYAVEAHFKHKP

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

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	;(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate ;
Molecular weight formula_weight	826.5 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3mdba_
Class class	b — All beta proteins
Fold Fold fold	b.26 — SMAD/FHA domain
Superfamily Superfamily superfamily	b.26.1 — SMAD/FHA domain
Family Family family	b.26.1.0 — automated matches

Domain ID domain_id	d3mdbb_
Class class	b — All beta proteins
Fold Fold fold	b.26 — SMAD/FHA domain
Superfamily Superfamily superfamily	b.26.1 — SMAD/FHA domain
Family Family family	b.26.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3mdbA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3mdbB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3mdbC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	150 — Arf GTPase activating protein

Domain ID domain_id	3mdbC02
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	3mdbC03
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	3mdbD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	150 — Arf GTPase activating protein

Domain ID domain_id	3mdbD02
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	3mdbD03
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)

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Unit-cell length a length_a	115.797 Å
Unit-cell length b length_b	115.797 Å
Unit-cell length c length_c	189.269 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.952 Å
Low-resolution limit resolution_low	29.437 Å
R factor r_factor	0.2270
R_work r_work	0.2250
R_free r_free	0.2770

Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4

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

Kinesin-like protein KIF13B

State in the Current Structure

Other States of the Same Protein in the Database

Arf-GAP with dual PH domain-containing protein 1

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4

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

Kinesin-like protein KIF13B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Arf-GAP with dual PH domain-containing protein 1

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)