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2kdc

NMR Solution Structure of E. coli diacylglycerol kinase (DAGK) in DPC micelles

Method: SOLUTION NMR
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Diacylglycerol kinase

Escherichia coli

UniProt P0ABN1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 3 No other associated polymer Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
2kdc 3ze3 3ze3 3ze4 3ze5 4bpd 4bpd 4brb 4brb 4brr 4brr 4cjz

29 assemblies; showing the first 12

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name KDGL_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–121； UniProt 2–122 Author chain B； PDBConstruct 1–121； UniProt 2–122 Author chain C； PDBConstruct 1–121； UniProt 2–122

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_id2kdc
Deposition date deposition_date2009-01-06
Structure title titleNMR Solution Structure of E. coli diacylglycerol kinase (DAGK) in DPC micelles
Keywords keywordsMembrane Protein, Kinase, DAGK, Cell inner membrane, Cell membrane, Membrane, Phospholipid biosynthesis, Transferase, Transmembrane; TRANSFERASE
Experimental Method methodSOLUTION NMR
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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.

2kdc__assembly_1__model_10

Assembly 1 · Model 10 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2kdc__assembly_1__model_10 | I(q)

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

2kdc__assembly_1__model_10 | 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）24.79 Å
Rg (electron density)23.79 Å
Total Rg24.42 Å
Atom count5658
Residues363
Excluded volume50420 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2kdc__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 2 2kdc__assembly_1__model_2 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 3 2kdc__assembly_1__model_3 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 4 2kdc__assembly_1__model_4 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 5 2kdc__assembly_1__model_5 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 6 2kdc__assembly_1__model_6 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 7 2kdc__assembly_1__model_7 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 8 2kdc__assembly_1__model_8 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 9 2kdc__assembly_1__model_9 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 10 2kdc__assembly_1__model_10 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 11 2kdc__assembly_1__model_11 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 12 2kdc__assembly_1__model_12 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 13 2kdc__assembly_1__model_13 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 14 2kdc__assembly_1__model_14 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 15 2kdc__assembly_1__model_15 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 16 2kdc__assembly_1__model_16 trimeric （3） 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 (1)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2kdca_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.62 — Diacylglycerol kinase (DgkA)-like
Superfamily Superfamily superfamilyf.62.1 — Diacylglycerol kinase (DgkA)-like
Family Family familyf.62.1.1 — Diacylglycerol kinase (DgkA)-like
Domain ID domain_idd2kdcb_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.62 — Diacylglycerol kinase (DgkA)-like
Superfamily Superfamily superfamilyf.62.1 — Diacylglycerol kinase (DgkA)-like
Family Family familyf.62.1.1 — Diacylglycerol kinase (DgkA)-like
Domain ID domain_idd2kdcc_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.62 — Diacylglycerol kinase (DgkA)-like
Superfamily Superfamily superfamilyf.62.1 — Diacylglycerol kinase (DgkA)-like
Family Family familyf.62.1.1 — Diacylglycerol kinase (DgkA)-like

CATH v4.4 (3 domains)

Domain ID domain_id2kdcA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3830 — Diacylglycerol kinase fold
Homologous superfamily homologous superfamily10 — Diacylglycerol kinase (DAGK) domain
Domain ID domain_id2kdcB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3830 — Diacylglycerol kinase fold
Homologous superfamily homologous superfamily10 — Diacylglycerol kinase (DAGK) domain
Domain ID domain_id2kdcC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3830 — Diacylglycerol kinase fold
Homologous superfamily homologous superfamily10 — Diacylglycerol kinase (DAGK) domain
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7. Citations (1)