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7ea9

Crystal Structure of human lysyl-tRNA synthetase Y145H mutant

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

Lysine--tRNA ligase

Homo sapiens

UniProt Q15046

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE × 2 GLYCEROL × 2 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE × 2 GLYCEROL × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
3bju 3bju 6chd 6ilh 7ea9 7ea9 8hyr 8xp4

8 assemblies

Homotetramer
3bju

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
4dpg 4dpg 4dpg 4dpg 4ycu 4ycw 4ycw 6ild 9dow 9dpa 9dpb 9dpl

12 assemblies

View Construct and Data Evidence
UniProt name SYK_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–513； UniProt 70–581 Author chain B； PDBConstruct 2–513； UniProt 70–581 Author chain C； PDBConstruct 2–513； UniProt 70–581 Author chain D； PDBConstruct 2–513； UniProt 70–581

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_id7ea9
Deposition date deposition_date2021-03-06
Structure title titleCrystal Structure of human lysyl-tRNA synthetase Y145H mutant
Keywords keywordslysyl-tRNA synthetase, LysRS, disease related mutant, LIGASE; LIGASE
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.

7ea9__assembly_1__model_1

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

Download this curve (.dat)

7ea9__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.

7ea9__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）32.18 Å
Rg (electron density)31.51 Å
Total Rg32.05 Å
Atom count8017
Residues1002
Excluded volume143280 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7ea9__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 7ea9__assembly_2__model_1 dimeric （2） 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 (4)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd7ea9a1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.0 — automated matches
Domain ID domain_idd7ea9a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.0 — automated matches
Domain ID domain_idd7ea9b1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.0 — automated matches
Domain ID domain_idd7ea9b2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.0 — automated matches
Domain ID domain_idd7ea9c1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.0 — automated matches
Domain ID domain_idd7ea9c2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.0 — automated matches
Domain ID domain_idd7ea9d1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.0 — automated matches
Domain ID domain_idd7ea9d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.0 — automated matches
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7. Citations (1)