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5cb5

Structural Insights into the Mechanism of Escherichia coli Ymdb

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

O-acetyl-ADP-ribose deacetylase

Escherichia coli K12

UniProt P0A8D6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
10 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
11 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 ACETATE ION × 1 water × 1 Consistent with protein count
12 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
13 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
14 Protein monomer Monomer Protein 1 SULFATE ION × 1 ;[(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanoate ; × 1 water × 1 Consistent with protein count
15 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
16 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
17 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
18 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 ACETATE ION × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 ACETATE ION × 1 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
6 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
7 Protein monomer Monomer Protein 1 SULFATE ION × 1 ;[(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanoate ; × 1 water × 1 Consistent with protein count
8 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count
9 Protein monomer Monomer Protein 1 ADENOSINE-5-DIPHOSPHORIBOSE × 1 SULFATE ION × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1spv 5cb3 5cb5 5cb5 5cb5 5cb5 5cb5 5cb5 5cb5 5cb5 5cb5 5cb5

20 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name YMDB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–183； UniProt 1–177 Author chain B； PDBConstruct 7–183； UniProt 1–177 Author chain C； PDBConstruct 7–183； UniProt 1–177 Author chain D； PDBConstruct 7–183； UniProt 1–177 Author chain E； PDBConstruct 7–183； UniProt 1–177 Author chain F； PDBConstruct 7–183； UniProt 1–177 Author chain G； PDBConstruct 7–183； UniProt 1–177 Author chain H； PDBConstruct 7–183； UniProt 1–177 Author chain I； PDBConstruct 7–183； UniProt 1–177 Author chain J； PDBConstruct 7–183； UniProt 1–177 Author chain K； PDBConstruct 7–183； UniProt 1–177 Author chain L； PDBConstruct 7–183； UniProt 1–177 Author chain M； PDBConstruct 7–183； UniProt 1–177 Author chain N； PDBConstruct 7–183； UniProt 1–177 Author chain O； PDBConstruct 7–183； UniProt 1–177 Author chain P； PDBConstruct 7–183； UniProt 1–177 Author chain Q； PDBConstruct 7–183； UniProt 1–177 Author chain R； PDBConstruct 7–183； UniProt 1–177

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_id5cb5
Deposition date deposition_date2015-06-30
Structure title titleStructural Insights into the Mechanism of Escherichia coli Ymdb
Keywords keywordsdeacetylase, ADPr, OAADPr, macro domain, 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.

5cb5__assembly_1__model_1

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

Download this curve (.dat)

5cb5__assembly_1__model_1 | I(q)

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

5cb5__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）16.19 Å
Rg (electron density)14.88 Å
Total Rg15.98 Å
Atom count1322
Residues173
Excluded volume23353 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5cb5__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5cb5__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5cb5__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5cb5__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 5cb5__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 5cb5__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 5cb5__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 5cb5__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 5cb5__assembly_9__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 5cb5__assembly_10__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
11 1 5cb5__assembly_11__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
12 1 5cb5__assembly_12__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
13 1 5cb5__assembly_13__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
14 1 5cb5__assembly_14__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
15 1 5cb5__assembly_15__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
16 1 5cb5__assembly_16__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
17 1 5cb5__assembly_17__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
18 1 5cb5__assembly_18__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) 36 domains

SCOP 2.08 (18 domains)

Domain ID domain_idd5cb5a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5c_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5d_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5e_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5f_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5g_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5h_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5i_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5j_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5k_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5l_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5m_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5n_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5o_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5p_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5q_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain
Domain ID domain_idd5cb5r_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain

CATH v4.4 (18 domains)

Domain ID domain_id5cb5A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5E00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5F00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5G00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5H00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5I00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5J00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5K00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5L00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5M00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5N00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5O00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5P00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5Q00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id5cb5R00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
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7. Citations (1)