SAXSdb — 3vyt

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

Hydrogenase expression/formation protein HypC

Thermococcus kodakarensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Hydrogenase expression/formation protein HypD × 2 （Q5JII1） Hydrogenase expression/formation protein HypE × 2 （Q5JII7） IRON/SULFUR CLUSTER × 2 MAGNESIUM ION × 10 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5JII0_PYRKO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–74； UniProt 2–75

Hydrogenase expression/formation protein HypD

Thermococcus kodakarensis

UniProt Q5JII1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Hydrogenase expression/formation protein HypC × 2 （Q5JII0） Hydrogenase expression/formation protein HypE × 2 （Q5JII7） IRON/SULFUR CLUSTER × 2 MAGNESIUM ION × 10 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5JII1_PYRKO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–372； UniProt 1–372

Hydrogenase expression/formation protein HypE

Thermococcus kodakarensis

UniProt Q5JII7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Hydrogenase expression/formation protein HypC × 2 （Q5JII0） Hydrogenase expression/formation protein HypD × 2 （Q5JII1） IRON/SULFUR CLUSTER × 2 MAGNESIUM ION × 10 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5JII7_PYRKO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–338； UniProt 1–338

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	3vyt
Deposition date deposition_date	2012-10-02
Structure title title	Crystal structure of the HypC-HypD-HypE complex (form I inward)
Keywords keywords	[NiFe] hydrogenase maturation, METAL BINDING PROTEIN-TRANSFERASE complex; METAL BINDING PROTEIN/TRANSFERASE
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.

3vyt__assembly_1__model_1

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

Download this curve (.dat)

3vyt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vyt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.53 Å
Rg (electron density)	39.56 Å
Total Rg	39.72 Å
Atom count	11374
Residues	1512
Excluded volume	204690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vyt__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	Hydrogenase expression/formation protein HypC
Molecular weight formula_weight	8133.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5902

CLAVPGKVIEVNGPVAVVDFGGVKREVRLDLMPDTKPGDWVIVHTGFAIEKLDEKKAMEILEAWAEVEKAMEGF

Source Source

Source organism organism	Thermococcus kodakarensis
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Hydrogenase expression/formation protein HypD
Molecular weight formula_weight	41925.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEEPFEAYRSREVAMKLVEKIREEAKTLDGEIRIMHVCGTHEDTVTRHGIRSLLPENVKVVSGPGCPVCITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYKIPTPMGSFADLKSEGFDVRIVYGIFDTYRIAKENPDKTVVHFSPGFETTTAPAAGMLNVAAQEELENFKIYSVHRLTPPAVEVLLKQGTVFQGLIAPGHVSTIIGVKGWEYLTEKYGIPQVVAGFEPNDVLMAILMLIRMYKEGEARIINEYERAVKYEGNVVAQKMIDKFFEVVDAKWRALGVFPKSGLELRKEWKDFEIRSFYKVEVPKNLPDLEKGCRCGAVLRGLALPTDCPLFGKTCTPRHPVGPCMVSYEGTCQIFYKYGVLF

Source Source

Source organism organism	Thermococcus kodakarensis
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Hydrogenase expression/formation protein HypE
Molecular weight formula_weight	35954.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGEKIKLEHGAGGEIMEELLRDVILKTLTLKSAGGIGLDALDDGATIPFGDKHIVFTIDGHTVKPLFFPGGDIGRLAVSGTVNDLAVMGAEPIALANSMIIGEGLDMEVLKRVLKSMDETAREVPVPIVTGDTKVVEDKIEMFVITAGIGIAEHPVSDAGAKVGDAVLVSGTIGDHGIALMSHREGIAFETELKSDVAPIWDVVKAVAETIGWENIHAMKDPTRAGLSNALNEIARKSNVGILVREADIPIRPEVRAASEMLGISPYDVANEGKVVMVVAREYAEEALEAMRKTEKGRNAAIIGEVIADYRGKVLLETGIGGKRFMEPPEGDPVPRIC

Source Source

Source organism organism	Thermococcus kodakarensis
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	153

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3vyta_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.14 — HupF/HypC-like
Family Family family	b.40.14.1 — HupF/HypC-like

CATH v4.4 (6 domains)

Domain ID domain_id	3vytA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3vytB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11750 — HypD, alpha/beta domain 1

Domain ID domain_id	3vytB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11740 — HypD, alpha/beta domain 2

Domain ID domain_id	3vytB03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	20 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3vytC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	3vytC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

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Unit-cell length a length_a	78.333 Å
Unit-cell length b length_b	99.412 Å
Unit-cell length c length_c	103.923 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	34.790 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2530

Crystal structure of the HypC-HypD-HypE complex (form I inward)

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

Hydrogenase expression/formation protein HypC

State in the Current Structure

Other States of the Same Protein in the Database

Hydrogenase expression/formation protein HypD

State in the Current Structure

Other States of the Same Protein in the Database

Hydrogenase expression/formation protein HypE

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

3vyt__assembly_1__model_1

3vyt__assembly_1__model_1 | I(q)

3vyt__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) 7 domains

SCOP 2.08 (1 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the HypC-HypD-HypE complex (form I inward)

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

Hydrogenase expression/formation protein HypC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hydrogenase expression/formation protein HypD

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hydrogenase expression/formation protein HypE

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

3vyt__assembly_1__model_1

3vyt__assembly_1__model_1 | I(q)

3vyt__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) 7 domains

SCOP 2.08 (1 domains)

CATH v4.4 (6 domains)

7. Citations (1)