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2dxb

Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Thiocyanate hydrolase subunit alpha

Thiobacillus thioparus

UniProt O66187

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 12 Thiocyanate hydrolase subunit beta × 4 （O66186） Thiocyanate hydrolase subunit gamma × 4 （O66188） COBALT (III) ION × 4 PHOSPHATE ION × 4 water × 12 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 12 Thiocyanate hydrolase subunit beta × 4 （O66186） Thiocyanate hydrolase subunit gamma × 4 （O66188） COBALT (III) ION × 4 PHOSPHATE ION × 4 water × 12 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2dd4 2dd5 2dxb 2dxb 2dxc 2zzd 3vyg

7 assemblies

View Construct and Data Evidence
UniProt name SCNA_THITI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–126； UniProt 0–125 Author chain D； PDBConstruct 1–126； UniProt 0–125 Author chain G； PDBConstruct 1–126； UniProt 0–125 Author chain J； PDBConstruct 1–126； UniProt 0–125 Author chain M； PDBConstruct 1–126； UniProt 0–125 Author chain P； PDBConstruct 1–126； UniProt 0–125 Author chain S； PDBConstruct 1–126； UniProt 0–125 Author chain V； PDBConstruct 1–126； UniProt 0–125

Thiocyanate hydrolase subunit beta

Thiobacillus thioparus

UniProt O66186

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 12 Thiocyanate hydrolase subunit alpha × 4 （O66187） Thiocyanate hydrolase subunit gamma × 4 （O66188） COBALT (III) ION × 4 PHOSPHATE ION × 4 water × 12 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 12 Thiocyanate hydrolase subunit alpha × 4 （O66187） Thiocyanate hydrolase subunit gamma × 4 （O66188） COBALT (III) ION × 4 PHOSPHATE ION × 4 water × 12 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2dd4 2dd5 2dxb 2dxb 2dxc 2zzd 3vyg

7 assemblies

View Construct and Data Evidence
UniProt name SCNB_THITI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–157； UniProt 0–156 Author chain E； PDBConstruct 1–157； UniProt 0–156 Author chain H； PDBConstruct 1–157； UniProt 0–156 Author chain K； PDBConstruct 1–157； UniProt 0–156 Author chain N； PDBConstruct 1–157； UniProt 0–156 Author chain Q； PDBConstruct 1–157； UniProt 0–156 Author chain T； PDBConstruct 1–157； UniProt 0–156 Author chain W； PDBConstruct 1–157； UniProt 0–156

Thiocyanate hydrolase subunit gamma

Thiobacillus thioparus

UniProt O66188

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 12 Thiocyanate hydrolase subunit alpha × 4 （O66187） Thiocyanate hydrolase subunit beta × 4 （O66186） COBALT (III) ION × 4 PHOSPHATE ION × 4 water × 12 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 12 Thiocyanate hydrolase subunit alpha × 4 （O66187） Thiocyanate hydrolase subunit beta × 4 （O66186） COBALT (III) ION × 4 PHOSPHATE ION × 4 water × 12 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2dd4 2dd5 2dxb 2dxb 2dxc 2zzd 3vyg

7 assemblies

View Construct and Data Evidence
UniProt name SCNC_THITI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–243； UniProt 0–242 Author chain F； PDBConstruct 1–243； UniProt 0–242 Author chain I； PDBConstruct 1–243； UniProt 0–242 Author chain L； PDBConstruct 1–243； UniProt 0–242 Author chain O； PDBConstruct 1–243； UniProt 0–242 Author chain R； PDBConstruct 1–243； UniProt 0–242 Author chain U； PDBConstruct 1–243； UniProt 0–242 Author chain X； PDBConstruct 1–243； UniProt 0–242

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_id2dxb
Deposition date deposition_date2006-08-25
Structure title titleRecombinant thiocyanate hydrolase comprising partially-modified cobalt centers
Keywords keywords;hydrolase, cobalt, metalloprotein, sulfenic acid, sulfinic acid, nitrile hydratase, thiocyanate, carbonyl sulfide, claw setting, protein, enzyme, complex, model complex, non-corrin, post-translational modification, sulfenate, sulfinate ;; HYDROLASE
Experimental Method methodX-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.

2dxb__assembly_1__model_1

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

Download this curve (.dat)

2dxb__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2dxb__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）38.30 Å
Rg (electron density)37.70 Å
Total Rg38.23 Å
Atom count15725
Residues1946
Excluded volume278970 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2dxb__assembly_1__model_1 dodecameric （12） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2dxb__assembly_2__model_1 dodecameric （12） 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 (6)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id2dxbA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2dxbB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily20 — Nitrile hydratase, beta subunit
Domain ID domain_id2dxbC00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma
Domain ID domain_id2dxbD00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2dxbE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily20 — Nitrile hydratase, beta subunit
Domain ID domain_id2dxbF00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma
Domain ID domain_id2dxbG00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2dxbH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily20 — Nitrile hydratase, beta subunit
Domain ID domain_id2dxbI00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma
Domain ID domain_id2dxbJ00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2dxbK00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily20 — Nitrile hydratase, beta subunit
Domain ID domain_id2dxbL00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma
Domain ID domain_id2dxbM00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2dxbN00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily20 — Nitrile hydratase, beta subunit
Domain ID domain_id2dxbO00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma
Domain ID domain_id2dxbP00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2dxbQ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily20 — Nitrile hydratase, beta subunit
Domain ID domain_id2dxbR00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma
Domain ID domain_id2dxbS00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2dxbT00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily20 — Nitrile hydratase, beta subunit
Domain ID domain_id2dxbU00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma
Domain ID domain_id2dxbV00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2dxbW00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily20 — Nitrile hydratase, beta subunit
Domain ID domain_id2dxbX00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma
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7. Citations (1)