4a51

Crystal structure of human kinesin Eg5 in complex with 1-(3-(((2-Aminoethyl)thio)diphenylmethyl)phenyl)ethanone hydrochloride

Method: X-RAY DIFFRACTION

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

KINESIN-LIKE PROTEIN KIF11

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1-(3-{[(2-aminoethyl)sulfanyl](diphenyl)methyl}phenyl)ethanone × 1 CHLORIDE ION × 4 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1-(3-{[(2-aminoethyl)sulfanyl](diphenyl)methyl}phenyl)ethanone × 1 CHLORIDE ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1-(3-{[(2-aminoethyl)sulfanyl](diphenyl)methyl}phenyl)ethanone × 1 CHLORIDE ION × 3 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1-(3-{[(2-aminoethyl)sulfanyl](diphenyl)methyl}phenyl)ethanone × 1 CHLORIDE ION × 2 SULFATE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1-(3-{[(2-aminoethyl)sulfanyl](diphenyl)methyl}phenyl)ethanone × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1-(3-{[(2-aminoethyl)sulfanyl](diphenyl)methyl}phenyl)ethanone × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1-(3-{[(2-aminoethyl)sulfanyl](diphenyl)methyl}phenyl)ethanone × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KIF11_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–368； UniProt 1–368 Author chain B； PDBConstruct 1–368； UniProt 1–368 Author chain C； PDBConstruct 1–368； UniProt 1–368 Author chain D； PDBConstruct 1–368； UniProt 1–368 Author chain E； PDBConstruct 1–368； UniProt 1–368 Author chain F； PDBConstruct 1–368； UniProt 1–368 Author chain G； PDBConstruct 1–368； UniProt 1–368

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	4a51
Deposition date deposition_date	2011-10-24
Structure title title	Crystal structure of human kinesin Eg5 in complex with 1-(3-(((2-Aminoethyl)thio)diphenylmethyl)phenyl)ethanone hydrochloride
Keywords keywords	CELL CYCLE, MITOSIS, INHIBITOR, KSP; CELL CYCLE
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.

4a51__assembly_1__model_1

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

Download this curve (.dat)

4a51__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4a51__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.98 Å
Rg (electron density)	19.76 Å
Total Rg	20.71 Å
Atom count	2574
Residues	322
Excluded volume	45914 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4a51__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4a51__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4a51__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4a51__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4a51__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4a51__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4a51__assembly_7__model_1`	monomeric （1）	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 (7)

Entity 1 Entity 1 polymer

Description description	KINESIN-LIKE PROTEIN KIF11
Molecular weight formula_weight	41055.6 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	18210

MASQPNSSAKKKEEKGKNIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADKSSRKTYTFDMVFGASTKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEGERSPNEEYTWEEDPLAGIIPRTLHQIFEKLTDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDPRNKRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETTIDGEELVKIGKLNLVDLAGSENIGRSGAVDKRAREAGNINQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAKNILNKPEVNQK

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 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	1-(3-{[(2-aminoethyl)sulfanyl](diphenyl)methyl}phenyl)ethanone
Molecular weight formula_weight	361.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d4a51a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.9 — Motor proteins

Domain ID domain_id	d4a51b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.9 — Motor proteins

Domain ID domain_id	d4a51c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.9 — Motor proteins

Domain ID domain_id	d4a51d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.9 — Motor proteins

Domain ID domain_id	d4a51e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.9 — Motor proteins

Domain ID domain_id	d4a51f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.9 — Motor proteins

Domain ID domain_id	d4a51g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.9 — Motor proteins

CATH v4.4 (7 domains)

Domain ID domain_id	4a51A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	850 — Kinesin
Homologous superfamily homologous superfamily	10 — Kinesin motor domain

Domain ID domain_id	4a51B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	850 — Kinesin
Homologous superfamily homologous superfamily	10 — Kinesin motor domain

Domain ID domain_id	4a51C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	850 — Kinesin
Homologous superfamily homologous superfamily	10 — Kinesin motor domain

Domain ID domain_id	4a51D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	850 — Kinesin
Homologous superfamily homologous superfamily	10 — Kinesin motor domain

Domain ID domain_id	4a51E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	850 — Kinesin
Homologous superfamily homologous superfamily	10 — Kinesin motor domain

Domain ID domain_id	4a51F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	850 — Kinesin
Homologous superfamily homologous superfamily	10 — Kinesin motor domain

Domain ID domain_id	4a51G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	850 — Kinesin
Homologous superfamily homologous superfamily	10 — Kinesin motor domain

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Unit-cell length a length_a	145.840 Å
Unit-cell length b length_b	156.400 Å
Unit-cell length c length_c	170.160 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	28

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

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	29.991 Å
R factor r_factor	0.2237
R_work r_work	0.2206
R_free r_free	0.2804

Crystal structure of human kinesin Eg5 in complex with 1-(3-(((2-Aminoethyl)thio)diphenylmethyl)phenyl)ethanone hydrochloride

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

KINESIN-LIKE PROTEIN KIF11

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

4a51__assembly_1__model_1

4a51__assembly_1__model_1 | I(q)

4a51__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Crystal structure of human kinesin Eg5 in complex with 1-(3-(((2-Aminoethyl)thio)diphenylmethyl)phenyl)ethanone hydrochloride

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

KINESIN-LIKE PROTEIN KIF11

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

4a51__assembly_1__model_1

4a51__assembly_1__model_1 | I(q)

4a51__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)