1kyq

Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis.

Method: X-RAY DIFFRACTION

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

Siroheme biosynthesis protein MET8

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MET8_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–274； UniProt 1–274 Author chain B； PDBConstruct 1–274； UniProt 1–274 Author chain C； PDBConstruct 1–274； UniProt 1–274

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	1kyq
Deposition date deposition_date	2002-02-05
Structure title title	Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis.
Keywords keywords	homodimer, OXIDOREDUCTASE, LYASE; OXIDOREDUCTASE, LYASE
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.

1kyq__assembly_1__model_1

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

Download this curve (.dat)

1kyq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kyq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.54 Å
Rg (electron density)	26.57 Å
Total Rg	27.16 Å
Atom count	4447
Residues	523
Excluded volume	79495 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kyq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1kyq__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 (3)

Entity 1 Entity 1 polymer

Description description	Siroheme biosynthesis protein MET8
Molecular weight formula_weight	32289.3 kDa
EC 编号 ec_number	1.-.-.-, 4.99.1.1
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	7289

MVKSLQLAHQLKDKRILLIGGGEVGLTRLYKLMPTGCKLTLVSPDLHKSIIPKFGKFIQNKDQPDYREDAKRFINPNWDPTKNEIYEYIRSDFKDEYLDLENENDAWYIIMTCIPDHPESARIYHLCKERFGKQQLVNVADKPDLCDFYFGANLEIGDRLQILISTNGLSPRFGALVRDEIRNLFTQMGDLALEDAVVKLGELRRGIRLLAPDDKDVKYRMDWARRCTDLFGIQHCHNIDVKRLLDLFKVMFQEQNCSLQFPPRERLLSEYCSS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	614

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1kyqa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.11 — Siroheme synthase N-terminal domain-like

Domain ID domain_id	d1kyqa2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.37 — Siroheme synthase middle domains-like
Superfamily Superfamily superfamily	e.37.1 — Siroheme synthase middle domains-like
Family Family family	e.37.1.1 — Siroheme synthase middle domains-like

Domain ID domain_id	d1kyqb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.11 — Siroheme synthase N-terminal domain-like

Domain ID domain_id	d1kyqb2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.37 — Siroheme synthase middle domains-like
Superfamily Superfamily superfamily	e.37.1 — Siroheme synthase middle domains-like
Family Family family	e.37.1.1 — Siroheme synthase middle domains-like

Domain ID domain_id	d1kyqc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.11 — Siroheme synthase N-terminal domain-like

Domain ID domain_id	d1kyqc2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.37 — Siroheme synthase middle domains-like
Superfamily Superfamily superfamily	e.37.1 — Siroheme synthase middle domains-like
Family Family family	e.37.1.1 — Siroheme synthase middle domains-like

CATH v4.4 (9 domains)

Domain ID domain_id	1kyqA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1kyqA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	110 — Sirohaem synthase, central domain

Domain ID domain_id	1kyqA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3280 — Siro heme synthase C-terminal domain-like
Homologous superfamily homologous superfamily	10 — Siroheme synthase; domain 3

Domain ID domain_id	1kyqB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1kyqB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	110 — Sirohaem synthase, central domain

Domain ID domain_id	1kyqB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3280 — Siro heme synthase C-terminal domain-like
Homologous superfamily homologous superfamily	10 — Siroheme synthase; domain 3

Domain ID domain_id	1kyqC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1kyqC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	110 — Sirohaem synthase, central domain

Domain ID domain_id	1kyqC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3280 — Siro heme synthase C-terminal domain-like
Homologous superfamily homologous superfamily	10 — Siroheme synthase; domain 3

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Unit-cell length a length_a	156.988 Å
Unit-cell length b length_b	80.856 Å
Unit-cell length c length_c	103.975 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	121.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2200
R_work r_work	0.2190
R_free r_free	0.2830

Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis.

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

Siroheme biosynthesis protein MET8

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

1kyq__assembly_1__model_1

1kyq__assembly_1__model_1 | I(q)

1kyq__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (2)

Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis.

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

Siroheme biosynthesis protein MET8

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

1kyq__assembly_1__model_1

1kyq__assembly_1__model_1 | I(q)

1kyq__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (2)