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1s64

Rat protein geranylgeranyltransferase type-I complexed with L-778,123 and a sulfate anion

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

Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit

Rattus norvegicus

UniProt Q04631

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Geranylgeranyl transferase type I beta subunit × 1 （P53610） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Geranylgeranyl transferase type I beta subunit × 1 （P53610） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 2 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Geranylgeranyl transferase type I beta subunit × 1 （P53610） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Geranylgeranyl transferase type I beta subunit × 1 （P53610） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 2 water × 2 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 Geranylgeranyl transferase type I beta subunit × 1 （P53610） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 2 water × 2 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 Geranylgeranyl transferase type I beta subunit × 1 （P53610） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3e30 3e32 3e33 3e34

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1d8d 1d8e 1fpp 1ft1 1ft2 1jcr 1jcs 1kzo 1kzp 1n4p 1n4p 1n4p

115 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PFTA_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–377； UniProt 1–377 Author chain C； PDBConstruct 1–377； UniProt 1–377 Author chain E； PDBConstruct 1–377； UniProt 1–377 Author chain G； PDBConstruct 1–377； UniProt 1–377 Author chain I； PDBConstruct 1–377； UniProt 1–377 Author chain K； PDBConstruct 1–377； UniProt 1–377

Geranylgeranyl transferase type I beta subunit

Rattus norvegicus

UniProt P53610

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit × 1 （Q04631） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit × 1 （Q04631） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 2 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit × 1 （Q04631） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit × 1 （Q04631） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 2 water × 2 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit × 1 （Q04631） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 2 water × 2 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit × 1 （Q04631） ZINC ION × 1 SULFATE ION × 1 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CHLORIDE ION × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1n4p 1n4p 1n4p 1n4p 1n4p 1n4p 1n4q 1n4q 1n4q 1n4q 1n4q 1n4q

72 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PGT1_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–377； UniProt 1–377 Author chain D； PDBConstruct 1–377； UniProt 1–377 Author chain F； PDBConstruct 1–377； UniProt 1–377 Author chain H； PDBConstruct 1–377； UniProt 1–377 Author chain J； PDBConstruct 1–377； UniProt 1–377 Author chain L； PDBConstruct 1–377； UniProt 1–377

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_id1s64
Deposition date deposition_date2004-01-22
Structure title titleRat protein geranylgeranyltransferase type-I complexed with L-778,123 and a sulfate anion
Keywords keywordsL-778, 123, protein geranylgeranyltransferase type-I, protein prenylation, lipid modification, drug, TRANSFERASE; TRANSFERASE
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.

1s64__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1s64__assembly_3__model_1 | I(q)

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

1s64__assembly_3__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）27.11 Å
Rg (electron density)26.24 Å
Total Rg26.98 Å
Atom count5404
Residues660
Excluded volume95548 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1s64__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1s64__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1s64__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1s64__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1s64__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 1s64__assembly_6__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 (8)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1s64a_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.6 — Protein prenylyltransferase
Family Family familya.118.6.1 — Protein prenylyltransferase
Domain ID domain_idd1s64b_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family familya.102.4.3 — Protein prenyltransferases
Domain ID domain_idd1s64c_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.6 — Protein prenylyltransferase
Family Family familya.118.6.1 — Protein prenylyltransferase
Domain ID domain_idd1s64d_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family familya.102.4.3 — Protein prenyltransferases
Domain ID domain_idd1s64e_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.6 — Protein prenylyltransferase
Family Family familya.118.6.1 — Protein prenylyltransferase
Domain ID domain_idd1s64f_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family familya.102.4.3 — Protein prenyltransferases
Domain ID domain_idd1s64g_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.6 — Protein prenylyltransferase
Family Family familya.118.6.1 — Protein prenylyltransferase
Domain ID domain_idd1s64h_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family familya.102.4.3 — Protein prenyltransferases
Domain ID domain_idd1s64i_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.6 — Protein prenylyltransferase
Family Family familya.118.6.1 — Protein prenylyltransferase
Domain ID domain_idd1s64j_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family familya.102.4.3 — Protein prenyltransferases
Domain ID domain_idd1s64k_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.6 — Protein prenylyltransferase
Family Family familya.118.6.1 — Protein prenylyltransferase
Domain ID domain_idd1s64l_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family familya.102.4.3 — Protein prenyltransferases

CATH v4.4 (12 domains)

Domain ID domain_id1s64A00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily120 — Protein prenylyltransferase
Domain ID domain_id1s64B00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1s64C00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily120 — Protein prenylyltransferase
Domain ID domain_id1s64D00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1s64E00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily120 — Protein prenylyltransferase
Domain ID domain_id1s64F00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1s64G00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily120 — Protein prenylyltransferase
Domain ID domain_id1s64H00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1s64I00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily120 — Protein prenylyltransferase
Domain ID domain_id1s64J00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1s64K00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily120 — Protein prenylyltransferase
Domain ID domain_id1s64L00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
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7. Citations (1)