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6eo0

Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29

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

NAD-dependent protein deacylase sirtuin-5, mitochondrial

Danio rerio

UniProt Q6DHI5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ZINC ION × 1 1,2-ETHANEDIOL × 1 ;3-[[(~{Z})-~{C}-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]sulfanyl-~{N}-[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]carbonimidoyl]amino]propanoic acid ; × 1 ;3-[[(2~{S},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2-[[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]amino]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]propanoic acid ; × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 ZINC ION × 1 1,2-ETHANEDIOL × 1 ;3-[[(2~{S},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2-[[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]amino]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]propanoic acid ; × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 ZINC ION × 1 1,2-ETHANEDIOL × 1 ;3-[[(2~{S},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2-[[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]amino]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]propanoic acid ; × 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 ZINC ION × 1 1,2-ETHANEDIOL × 1 ;3-[[(2~{S},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2-[[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]amino]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]propanoic acid ; × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
4utn 4utr 4utv 4utx 4utz 4uu7 4uu8 4uua 4uub 5ojo 6enx 6eo0

17 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4utn 4utr 4utv 4utx 4utz 4uu7 4uu8 4uua 4uub 5ojo 6fky 6fkz

13 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SIR5_DANRE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–277； UniProt 28–298 Author chain B； PDBConstruct 7–277； UniProt 28–298 Author chain C； PDBConstruct 7–277； UniProt 28–298 Author chain D； PDBConstruct 7–277； UniProt 28–298

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_id6eo0
Deposition date deposition_date2017-10-08
Structure title titleZebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29
Keywords keywordsHydrolase, PTM, inhibitor, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

6eo0__assembly_1__model_1

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

Download this curve (.dat)

6eo0__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6eo0__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）20.83 Å
Rg (electron density)20.01 Å
Total Rg21.01 Å
Atom count2214
Residues274
Excluded volume39156 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6eo0__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6eo0__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6eo0__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6eo0__assembly_4__model_1 monomeric （1） 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) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6eo0a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.5 — Sir2 family of transcriptional regulators
Domain ID domain_idd6eo0a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6eo0b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.5 — Sir2 family of transcriptional regulators
Domain ID domain_idd6eo0b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6eo0c1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.5 — Sir2 family of transcriptional regulators
Domain ID domain_idd6eo0c2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6eo0d1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.5 — Sir2 family of transcriptional regulators
Domain ID domain_idd6eo0d2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id6eo0A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id6eo0A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id6eo0B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id6eo0B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id6eo0C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id6eo0C02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id6eo0D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id6eo0D02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
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7. Citations (1)