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3pki

Human SIRT6 crystal structure in complex with ADP ribose

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

NAD-dependent deacetylase sirtuin-6

Homo sapiens

UniProt Q8N6T7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 UNKNOWN ATOM OR ION × 2 ZINC ION × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 SULFATE ION × 5 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 UNKNOWN ATOM OR ION × 6 ZINC ION × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 SULFATE ION × 3 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 UNKNOWN ATOM OR ION × 7 ZINC ION × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 SULFATE ION × 4 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 UNKNOWN ATOM OR ION × 3 ZINC ION × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 SULFATE ION × 3 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 UNKNOWN ATOM OR ION × 2 ZINC ION × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 SULFATE ION × 6 water × 1 Consistent with protein count
6 Protein monomer Monomer Protein 1 UNKNOWN ATOM OR ION × 6 ZINC ION × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 SULFATE ION × 2 water × 1 Consistent with protein count
7 Protein homooligomer Homooligomer Protein 3 UNKNOWN ATOM OR ION × 15 ZINC ION × 3 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 3 SULFATE ION × 12 water × 3 Consistent with protein count
8 Protein homooligomer Homooligomer Protein 3 UNKNOWN ATOM OR ION × 11 ZINC ION × 3 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 3 SULFATE ION × 11 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3k35 3k35 3k35 3k35 3k35 3k35 3pki 3pki 3pki 3pki 3pki 3pki

79 assemblies; showing the first 12

Homodimer
6qcj 6zu4 8cnm 8cno

4 assemblies

Homotetramer

None

Other homooligomers
3k35 3pki 3pki 3pkj 8i2b 8zvp 9g7h

7 assemblies

Heteromeric or nucleic-acid complex
3zg6 5y2f 7cl0 7cl1 8f86 8g57 8of4 9eil

8 assemblies

View Construct and Data Evidence
UniProt name SIRT6_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–355； UniProt 2–355 Author chain B； PDBConstruct 2–355； UniProt 2–355 Author chain C； PDBConstruct 2–355； UniProt 2–355 Author chain D； PDBConstruct 2–355； UniProt 2–355 Author chain E； PDBConstruct 2–355； UniProt 2–355 Author chain F； PDBConstruct 2–355； UniProt 2–355

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_id3pki
Deposition date deposition_date2010-11-11
Structure title titleHuman SIRT6 crystal structure in complex with ADP ribose
Keywords keywordsSIRT6, ADP ribose, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, HYDROLASE; 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.

Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3pki__assembly_1__model_1 monomeric （1） Excluded — —
Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2 1 3pki__assembly_2__model_1 monomeric （1） Excluded — —
Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
3 1 3pki__assembly_3__model_1 monomeric （1） Excluded — —
Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
4 1 3pki__assembly_4__model_1 monomeric （1） Excluded — —
Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
5 1 3pki__assembly_5__model_1 monomeric （1） Excluded — —
Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
6 1 3pki__assembly_6__model_1 monomeric （1） Excluded — —
Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
7 1 3pki__assembly_7__model_1 trimeric （3） Excluded — —
Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
8 1 3pki__assembly_8__model_1 trimeric （3） Excluded — —
Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
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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) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id3pkiA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id3pkiA02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily200 —
Domain ID domain_id3pkiB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id3pkiB02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily200 —
Domain ID domain_id3pkiC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id3pkiC02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily200 —
Domain ID domain_id3pkiD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id3pkiD02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily200 —
Domain ID domain_id3pkiE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id3pkiE02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily200 —
Domain ID domain_id3pkiF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id3pkiF02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily200 —
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7. Citations (1)