6m4w

Crystal structure of MBP fused split FKBP-FRB T2098L mutant in complex with rapamycin

Method: X-RAY DIFFRACTION

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

chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 其他Polymer 1	Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P62942） Serine/threonine-protein kinase mTOR × 1 （P42345） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 GLYCEROL × 1 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3 其他Polymer 1	Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P62942） Serine/threonine-protein kinase mTOR × 1 （P42345） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 water × 3	Consistent with protein count
3	Insufficient information	Heteromer	Protein 3 其他Polymer 1	Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P62942） Serine/threonine-protein kinase mTOR × 1 （P42345） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–369； UniProt 27–392 Author chain B； PDBConstruct 4–369； UniProt 27–392 Author chain C； PDBConstruct 4–369； UniProt 27–392

chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A

Homo sapiens

UniProt P62942

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 其他Polymer 1	Serine/threonine-protein kinase mTOR × 1 （P42345） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 GLYCEROL × 1 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3 其他Polymer 1	Serine/threonine-protein kinase mTOR × 1 （P42345） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 water × 3	Consistent with protein count
3	Insufficient information	Heteromer	Protein 3 其他Polymer 1	Serine/threonine-protein kinase mTOR × 1 （P42345） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FKB1A_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 374–405； UniProt 1–32 Author chain B； PDBConstruct 374–405； UniProt 1–32 Author chain C； PDBConstruct 374–405； UniProt 1–32 Author chain D； PDBConstruct 1–76； UniProt 33–108 Author chain E； PDBConstruct 1–76； UniProt 33–108 Author chain F； PDBConstruct 1–76； UniProt 33–108

Serine/threonine-protein kinase mTOR

Homo sapiens

UniProt P42345

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 其他Polymer 1	chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P0AEX9,P62942） Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P62942） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 GLYCEROL × 1 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3 其他Polymer 1	chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P0AEX9,P62942） Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P62942） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 water × 3	Consistent with protein count
3	Insufficient information	Heteromer	Protein 3 其他Polymer 1	chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P0AEX9,P62942） Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P62942） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTOR_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 3–95； UniProt 2021–2113 Author chain H； PDBConstruct 3–95； UniProt 2021–2113 Author chain I； PDBConstruct 3–95； UniProt 2021–2113

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	6m4w
Deposition date deposition_date	2020-03-09
Structure title title	Crystal structure of MBP fused split FKBP-FRB T2098L mutant in complex with rapamycin
Keywords keywords	Rapamycin, complex, kinase, isomerase; ISOMERASE
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.

6m4w__assembly_1__model_1

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

Download this curve (.dat)

6m4w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6m4w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.44 Å
Rg (electron density)	28.86 Å
Total Rg	29.58 Å
Atom count	4556
Residues	571
Excluded volume	81504 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6m4w__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6m4w__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6m4w__assembly_3__model_1`	trimeric （3）	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	chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
Molecular weight formula_weight	44074.9 kDa
EC 编号 ec_number	5.2.1.8
Mutation mutation	D-288A, K-287A, E-198A, N-197A, K-131A
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	13794

GSMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAAAMGVQVETISPGDGRTFPKRGQTCVVHYTGMLE

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	Peptidyl-prolyl cis-trans isomerase FKBP1A
Molecular weight formula_weight	8486.7 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

DGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

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 polymer

Description description	Serine/threonine-protein kinase mTOR
Molecular weight formula_weight	11447.1 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	T2098L
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I

GSILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEWCRKYMKSGNVKDLLQAWDLYYHVFRRISK

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 4 Entity 4 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	RAPAMYCIN IMMUNOSUPPRESSANT DRUG
Molecular weight formula_weight	914.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	191

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d6m4wa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d6m4wb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d6m4wc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d6m4wg1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.7 — FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
Family Family family	a.24.7.1 — FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)

Domain ID domain_id	d6m4wg2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6m4wh1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.7 — FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
Family Family family	a.24.7.1 — FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)

Domain ID domain_id	d6m4wh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6m4wi1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.7 — FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
Family Family family	a.24.7.1 — FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)

Domain ID domain_id	d6m4wi2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	6m4wA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	6m4wB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	6m4wC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	6m4wD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6m4wE01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6m4wF01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	127.546 Å
Unit-cell length b length_b	127.546 Å
Unit-cell length c length_c	278.557 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.110 Å
Low-resolution limit resolution_low	48.650 Å
R factor r_factor	0.2384
R_work r_work	0.2363
R_free r_free	0.2784

Crystal structure of MBP fused split FKBP-FRB T2098L mutant in complex with rapamycin

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

chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A

State in the Current Structure

Other States of the Same Protein in the Database

chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A

State in the Current Structure

Other States of the Same Protein in the Database

Serine/threonine-protein kinase mTOR

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

6m4w__assembly_1__model_1

6m4w__assembly_1__model_1 | I(q)

6m4w__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of MBP fused split FKBP-FRB T2098L mutant in complex with rapamycin

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

chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine/threonine-protein kinase mTOR

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

6m4w__assembly_1__model_1

6m4w__assembly_1__model_1 | I(q)

6m4w__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)