1w2w

Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits

Method: X-RAY DIFFRACTION

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

5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YP18_YEAST
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 1–211 Author chain E； PDBConstruct 1–211； UniProt 1–211 Author chain I； PDBConstruct 1–211； UniProt 1–211 Author chain M； PDBConstruct 1–211； UniProt 1–211 Author chain B； PDBConstruct 1–191； UniProt 221–411 Author chain F； PDBConstruct 1–191； UniProt 221–411 Author chain J； PDBConstruct 1–191； UniProt 221–411 Author chain N； PDBConstruct 1–191； UniProt 221–411

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	1w2w
Deposition date deposition_date	2004-07-09
Structure title title	Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits
Keywords keywords	ISOMERASE, EIF2B, METHIONINE SALVAGE PATHWAY, TRANSLATION INITIATION, OXIDOREDUCTASE; 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.

1w2w__assembly_1__model_1

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

Download this curve (.dat)

1w2w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w2w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.14 Å
Rg (electron density)	29.45 Å
Total Rg	29.98 Å
Atom count	6210
Residues	794
Excluded volume	111650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w2w__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1w2w__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
Molecular weight formula_weight	23353.1 kDa
EC 编号 ec_number	5.3.1.23
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M
Atom count atom_count	13350

MSLEAIVFDRSEPENVSVKVLDQLLLPYTTKYVPIHTIDDGYSVIKSMQVRGAPAIAIVGSLSVLTEVQLIKHNPTSDVATLYSLVNWESTKTVLNKRLDFLLSSRPTAVNLSNSLVEIKNILKSSSDLKAFDGSLYNYVCELIDEDLANNMKMGDNGAKYLIDVLQKDGFKDEFAVLTICNTGSLATSGYGTALGVIRSLWKDSLAKTDK

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 polymer

Description description	5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
Molecular weight formula_weight	21031.7 kDa
EC 编号 ec_number	5.3.1.23
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J,N

CPRMGHVFPLETRPYNQGSRLTAYELVYDKIPSTLITDSSIAYRIRTSPIPIKAAFVGADRIVRNGDTANKIGTLQLAVICKQFGIKFFVVAPKTTIDNVTETGDDIIVEERNPEEFKVVTGTVINPENGSLILNESGEPITGKVGIAPLEINVWNPAFDITPHELIDGIITEEGVFTKNSSGEFQLESLF

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 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	922

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1w2w.1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.5 — IF2B-like

Domain ID domain_id	d1w2w.2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.5 — IF2B-like

Domain ID domain_id	d1w2w.3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.5 — IF2B-like

Domain ID domain_id	d1w2w.4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.5 — IF2B-like

CATH v4.4 (8 domains)

Domain ID domain_id	1w2wA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	420 — translation initiation factor eif-2b, domain 1

Domain ID domain_id	1w2wB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10470 — Translation initiation factor eif-2b; domain 2

Domain ID domain_id	1w2wE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	420 — translation initiation factor eif-2b, domain 1

Domain ID domain_id	1w2wF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10470 — Translation initiation factor eif-2b; domain 2

Domain ID domain_id	1w2wI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	420 — translation initiation factor eif-2b, domain 1

Domain ID domain_id	1w2wJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10470 — Translation initiation factor eif-2b; domain 2

Domain ID domain_id	1w2wM00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	420 — translation initiation factor eif-2b, domain 1

Domain ID domain_id	1w2wN00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10470 — Translation initiation factor eif-2b; domain 2

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Unit-cell length a length_a	60.620 Å
Unit-cell length b length_b	105.450 Å
Unit-cell length c length_c	263.050 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1740
R_work r_work	0.1740
R_free r_free	0.1980

Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits

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

5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE

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

1w2w__assembly_1__model_1

1w2w__assembly_1__model_1 | I(q)

1w2w__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits

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

5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE

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

1w2w__assembly_1__model_1

1w2w__assembly_1__model_1 | I(q)

1w2w__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)