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1tnb

Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a substrate KKSKTKCVIF Peptide Derived from TC21

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

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 3 Geranylgeranyl transferase type I beta subunit × 1 （P53610） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Geranylgeranyl transferase type I beta subunit × 1 （P53610） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 CHLORIDE ION × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Geranylgeranyl transferase type I beta subunit × 1 （P53610） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 CHLORIDE ION × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Geranylgeranyl transferase type I beta subunit × 1 （P53610） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 CHLORIDE ION × 1 water × 3 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Geranylgeranyl transferase type I beta subunit × 1 （P53610） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 water × 3 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 Geranylgeranyl transferase type I beta subunit × 1 （P53610） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 water × 3 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 3 geranylgeranyltransferase type I alpha subunit × 1 （Q04631） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 geranylgeranyltransferase type I alpha subunit × 1 （Q04631） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 CHLORIDE ION × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 geranylgeranyltransferase type I alpha subunit × 1 （Q04631） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 CHLORIDE ION × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 geranylgeranyltransferase type I alpha subunit × 1 （Q04631） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 CHLORIDE ION × 1 water × 3 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 geranylgeranyltransferase type I alpha subunit × 1 （Q04631） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 water × 3 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 geranylgeranyltransferase type I alpha subunit × 1 （Q04631） Fusion protein × 1 ZINC ION × 1 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE × 1 water × 3 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_id1tnb
Deposition date deposition_date2004-06-11
Structure title titleRat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a substrate KKSKTKCVIF Peptide Derived from TC21
Keywords keywords;GGTase-I, geranylgeranyltransferase type-I, geranylgeranyl transferase, prenyltransferase, CaaX, TC21, Lipid modification, prenylation, substrate selectivity, 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.

1tnb__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1tnb__assembly_5__model_1 | I(q)

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

1tnb__assembly_5__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）27.02 Å
Rg (electron density)26.11 Å
Total Rg26.85 Å
Atom count5428
Residues665
Excluded volume96185 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1tnb__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1tnb__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1tnb__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1tnb__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1tnb__assembly_5__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 1tnb__assembly_6__model_1 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 (8)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1tnba_
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_idd1tnbb_
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_idd1tnbc_
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_idd1tnbd_
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_idd1tnbe_
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_idd1tnbf_
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_idd1tnbg_
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_idd1tnbh_
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_idd1tnbi_
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_idd1tnbj_
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_idd1tnbk_
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_idd1tnbl_
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_id1tnbA00
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_id1tnbB00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1tnbC00
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_id1tnbD00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1tnbE00
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_id1tnbF00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1tnbG00
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_id1tnbH00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1tnbI00
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_id1tnbJ00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1tnbK00
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_id1tnbL00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily20 —
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7. Citations (1)