1iwp

Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae

Method: X-RAY DIFFRACTION

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

Glycerol Dehydratase Alpha subunit

Klebsiella pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Glycerol Dehydratase Beta subunit × 2 （O08505） Glycerol Dehydratase Gamma subunit × 2 （Q59475） POTASSIUM ION × 2 S-1,2-PROPANEDIOL × 2 COBALAMIN × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q59476_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–555； UniProt 1–555 Author chain L； PDBConstruct 1–555； UniProt 1–555

Glycerol Dehydratase Beta subunit

Klebsiella pneumoniae

UniProt O08505

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Glycerol Dehydratase Alpha subunit × 2 （Q59476） Glycerol Dehydratase Gamma subunit × 2 （Q59475） POTASSIUM ION × 2 S-1,2-PROPANEDIOL × 2 COBALAMIN × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O08505_KLEPN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–194； UniProt 1–194 Author chain E； PDBConstruct 1–194； UniProt 1–194

Glycerol Dehydratase Gamma subunit

Klebsiella pneumoniae

UniProt Q59475

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Glycerol Dehydratase Alpha subunit × 2 （Q59476） Glycerol Dehydratase Beta subunit × 2 （O08505） POTASSIUM ION × 2 S-1,2-PROPANEDIOL × 2 COBALAMIN × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q59475_KLEPN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–141； UniProt 1–141 Author chain M； PDBConstruct 1–141； UniProt 1–141

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	1iwp
Deposition date deposition_date	2002-05-28
Structure title title	Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae
Keywords keywords	B12, GLYCEROL DEHYDRATASE, KLEBSIELLA PNEUMONIAE, COBALAMIN, RADICAL CATALYSIS, LYASE; 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.

1iwp__assembly_1__model_1

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

Download this curve (.dat)

1iwp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1iwp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.28 Å
Rg (electron density)	36.83 Å
Total Rg	37.10 Å
Atom count	13750
Residues	1754
Excluded volume	244080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1iwp__assembly_1__model_1`	hexameric （6）	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	Glycerol Dehydratase Alpha subunit
Molecular weight formula_weight	60714.6 kDa
EC 编号 ec_number	4.2.1.30
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,L
Atom count atom_count	14631

MKRSKRFAVLAQRPVNQDGLIGEWPEEGLIAMDSPFDPVSSVKVDNGLIVELDGKRRDQFDMIDRFIADYAINVERTEQAMRLEAVEIARMLVDIHVSREEIIAITTAITPAKAVEVMAQMNVVEMMMALQKMRARRTPSNQCHVTNLKDNPVQIAADAAEAGIRGFSEQETTVGIARYAPFNALALLVGSQCGRPGVLTQCSVEEATELELGMRGLTSYAETVSVYGTEAVFTDGDDTPWSKAFLASAYASRGLKMRYTSGTGSEALMGYSESKSMLYLESRCIFITKGAGVQGLQNGAVSCIGMTGAVPSGIRAVLAENLIASMLDLEVASANDQTFSHSDIRRTARTLMQMLPGTDFIFSGYSAVPNYDNMFAGSNFDAEDFDDYNILQRDLMVDGGLRPVTEAETIAIRQKAARAIQAVFRELGLPPIADEEVEAATYAHGSNEMPPRNVVEDLSAVEEMMKRNITGLDIVGALSRSGFEDIASNILNMLRQRVTGDYLQTSAILDRQFEVVSAVNDINDYQGPGTGYRISAERWAEIKNIPGVVQPDTIE

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Glycerol Dehydratase Beta subunit
Molecular weight formula_weight	21385.5 kDa
EC 编号 ec_number	4.2.1.30
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MQQTTQIQPSFTLKTREGGVASADERADEVVIGVGPAFDKHQHHTLIDMPHGAILKELIAGVEEEGLHARVVRILRTSDVSFMAWDAANLSGSGIGIGIQSKGTTVIHQRDLLPLSNLELFSQAPLLTLETYRQIGKNAARYARKESPSPVPVVNDQMVRPKFMAKAALFHIKETKHVVQDAEPVTLHIDLVRE

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Glycerol Dehydratase Gamma subunit
Molecular weight formula_weight	16128.4 kDa
EC 编号 ec_number	4.2.1.30
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,M

MSEKTMRVQDYPLATRCPEHILTPTGKPLTDITLEKVLSGEVGPQDVRISRQTLEYQAQIAEQMQRHAVARNFRRAAELIAIPDERILAIYNALRPFRSSQAELLAIADELEHTWHATVNAAFVRESAEVYQQRHKLRKGS

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	S-1,2-PROPANEDIOL
Molecular weight formula_weight	76.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	881

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1iwpa_
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.1.19.3 — Diol dehydratase, alpha subunit

Domain ID domain_id	d1iwpb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
Family Family family	c.51.3.1 — Diol dehydratase, beta subunit

Domain ID domain_id	d1iwpe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
Family Family family	c.51.3.1 — Diol dehydratase, beta subunit

Domain ID domain_id	d1iwpg_
Class class	a — All alpha proteins
Fold Fold fold	a.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamily	a.23.2 — Diol dehydratase, gamma subunit
Family Family family	a.23.2.1 — Diol dehydratase, gamma subunit

Domain ID domain_id	d1iwpl_
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.1.19.3 — Diol dehydratase, alpha subunit

Domain ID domain_id	d1iwpm_
Class class	a — All alpha proteins
Fold Fold fold	a.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamily	a.23.2 — Diol dehydratase, gamma subunit
Family Family family	a.23.2.1 — Diol dehydratase, gamma subunit

CATH v4.4 (6 domains)

Domain ID domain_id	1iwpA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	350 — Diol/glycerol dehydratase, large subunit

Domain ID domain_id	1iwpB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10150 — B12-dependent dehydatase associated subunit

Domain ID domain_id	1iwpE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10150 — B12-dependent dehydatase associated subunit

Domain ID domain_id	1iwpG02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
Homologous superfamily homologous superfamily	20 — Propanediol/glycerol dehydratase, small subunit

Domain ID domain_id	1iwpL00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	350 — Diol/glycerol dehydratase, large subunit

Domain ID domain_id	1iwpM02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
Homologous superfamily homologous superfamily	20 — Propanediol/glycerol dehydratase, small subunit

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Unit-cell length a length_a	81.380 Å
Unit-cell length b length_b	108.223 Å
Unit-cell length c length_c	113.141 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.75 °
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	2.100 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	—
R_work r_work	0.2090
R_free r_free	0.2470

Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae

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

Glycerol Dehydratase Alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Glycerol Dehydratase Beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Glycerol Dehydratase Gamma 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

1iwp__assembly_1__model_1

1iwp__assembly_1__model_1 | I(q)

1iwp__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae

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

Glycerol Dehydratase 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

Glycerol Dehydratase 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

Glycerol Dehydratase Gamma 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

1iwp__assembly_1__model_1

1iwp__assembly_1__model_1 | I(q)

1iwp__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)