5req

Methylmalonyl-COA MUTASE, Y89F Mutant, substrate complex

Method: X-RAY DIFFRACTION

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

PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)

Propionibacterium freudenreichii subsp. shermanii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT) × 1 （P11652） SUCCINYL(CARBADETHIA)-COENZYME A × 1 METHYLMALONYL(CARBADETHIA)-COENZYME A × 1 COBALAMIN × 1 GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT) × 1 （P11652） SUCCINYL(CARBADETHIA)-COENZYME A × 1 METHYLMALONYL(CARBADETHIA)-COENZYME A × 1 COBALAMIN × 1 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MUTB_PROFR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–727； UniProt 1–727 Author chain C； PDBConstruct 1–727； UniProt 1–727

PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)

Propionibacterium freudenreichii subsp. shermanii

UniProt P11652

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT) × 1 （P11653） SUCCINYL(CARBADETHIA)-COENZYME A × 1 METHYLMALONYL(CARBADETHIA)-COENZYME A × 1 COBALAMIN × 1 GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT) × 1 （P11653） SUCCINYL(CARBADETHIA)-COENZYME A × 1 METHYLMALONYL(CARBADETHIA)-COENZYME A × 1 COBALAMIN × 1 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MUTA_PROFR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–637； UniProt 1–637 Author chain D； PDBConstruct 1–637； UniProt 1–637

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	5req
Deposition date deposition_date	1998-08-03
Structure title title	Methylmalonyl-COA MUTASE, Y89F Mutant, substrate complex
Keywords keywords	ISOMERASE, MUTASE, INTRAMOLECULAR TRANSFERASE; 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.

5req__assembly_1__model_1

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

Download this curve (.dat)

5req__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5req__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.28 Å
Rg (electron density)	32.48 Å
Total Rg	33.09 Å
Atom count	10454
Residues	1344
Excluded volume	185460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5req__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5req__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 (7)

Entity 1 Entity 1 polymer

Description description	PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)
Molecular weight formula_weight	80121.9 kDa
EC 编号 ec_number	5.4.99.2
Mutation mutation	Y89F
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	22112

STLPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQFAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASLDA

Source Source

Source organism organism	Propionibacterium freudenreichii subsp. shermanii
NCBI taxonomy ID ncbi_taxonomy_id	1752
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)
Molecular weight formula_weight	69430.2 kDa
EC 编号 ec_number	5.4.99.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKRLTVHTVDGIDIVPMYRPKDAPKKLGYPGVAPFTRGTTVRNGDMDAWDVRALHEDPDEKFTRKAILEGLERGVTSLLLRVDPDAIAPEHLDEVLSDVLLEMTKVEVFSRYDQGAAAEALVSVYERSDKPAKDLALNLGLDPIGFAALQGTEPDLTVLGDWVRRLAKFSPDSRAVTIDANIYHNAGAGDVAELAWALATGAEYVRALVEQGFTATEAFDTINFRVTATHDQFLTIARLRALREAWARIGEVFGVDEDKRGARQNAITSWRELTREDPYVNILRGSIATFSASVGGAESITTLPFTQALGLPEDDFPLRIARNTGIVLAEEVNIGRVNDPAGGSYYVESLTRSLADAAWKEFQEVEKLGGMSKAVMTEHVTKVLDACNAERAKRLANRKQPITAVSEFPMIGARSIETKPFPAAPARKGLAWHRDSEVFEQLMDRSTSVSERPKVFLACLGTRRDFGGREGFSSPVWHIAGIDTPQVEGGTTAEIVEAFKKSGAQVADLCSSAKVYAQQGLEVAKALKAAGAKALYLSGAFKEFGDDAAEAEKLIDGRLFMGMDVVDTLSSTLDILGVAK

Source Source

Source organism organism	Propionibacterium freudenreichii subsp. shermanii
NCBI taxonomy ID ncbi_taxonomy_id	1752
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SUCCINYL(CARBADETHIA)-COENZYME A
Molecular weight formula_weight	849.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	METHYLMALONYL(CARBADETHIA)-COENZYME A
Molecular weight formula_weight	849.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	2

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	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1094

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5reqa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

Domain ID domain_id	d5reqa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
Family Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

Domain ID domain_id	d5reqb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

Domain ID domain_id	d5reqb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
Family Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

Domain ID domain_id	d5reqc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

Domain ID domain_id	d5reqc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
Family Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

Domain ID domain_id	d5reqd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

Domain ID domain_id	d5reqd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
Family Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

CATH v4.4 (10 domains)

Domain ID domain_id	5reqA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

Domain ID domain_id	5reqA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	280 — Cobalamin-binding domain

Domain ID domain_id	5reqB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

Domain ID domain_id	5reqB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	280 — Cobalamin-binding domain

Domain ID domain_id	5reqB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	196 — Regulator of G-protein Signalling 4; domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5reqC01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

Domain ID domain_id	5reqC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	280 — Cobalamin-binding domain

Domain ID domain_id	5reqD01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

Domain ID domain_id	5reqD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	280 — Cobalamin-binding domain

Domain ID domain_id	5reqD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	196 — Regulator of G-protein Signalling 4; domain 1
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	120.200 Å
Unit-cell length b length_b	161.890 Å
Unit-cell length c length_c	88.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2560
R_work r_work	0.2460
R_free r_free	0.2920

Methylmalonyl-COA MUTASE, Y89F Mutant, substrate complex

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

PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)

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

5req__assembly_1__model_1

5req__assembly_1__model_1 | I(q)

5req__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 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) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Methylmalonyl-COA MUTASE, Y89F Mutant, substrate complex

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

PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)

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

5req__assembly_1__model_1

5req__assembly_1__model_1 | I(q)

5req__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 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) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. Citations (1)