1n4p

Protein Geranylgeranyltransferase type-I Complexed with Geranylgeranyl Diphosphate

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha

Rattus norvegicus

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-1 subunit beta × 1 （P53610） ZINC ION × 1 CHLORIDE ION × 1 GERANYLGERANYL DIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） ZINC ION × 1 CHLORIDE ION × 2 GERANYLGERANYL DIPHOSPHATE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） ZINC ION × 1 CHLORIDE ION × 1 GERANYLGERANYL DIPHOSPHATE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） ZINC ION × 1 CHLORIDE ION × 2 GERANYLGERANYL DIPHOSPHATE × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b × 1 ZINC ION × 1 CHLORIDE ION × 1 GERANYLGERANYL DIPHOSPHATE × 1 GERAN-8-YL GERAN × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 3	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b × 1 ZINC ION × 1 CHLORIDE ION × 2 GERANYLGERANYL DIPHOSPHATE × 1 GERAN-8-YL GERAN × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FNTA_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-1 subunit beta

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-1 subunit alpha × 1 （Q04631） ZINC ION × 1 CHLORIDE ION × 1 GERANYLGERANYL DIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha × 1 （Q04631） ZINC ION × 1 CHLORIDE ION × 2 GERANYLGERANYL DIPHOSPHATE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha × 1 （Q04631） ZINC ION × 1 CHLORIDE ION × 1 GERANYLGERANYL DIPHOSPHATE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha × 1 （Q04631） ZINC ION × 1 CHLORIDE ION × 2 GERANYLGERANYL DIPHOSPHATE × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha × 1 （Q04631） Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b × 1 ZINC ION × 1 CHLORIDE ION × 1 GERANYLGERANYL DIPHOSPHATE × 1 GERAN-8-YL GERAN × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 3	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha × 1 （Q04631） Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b × 1 ZINC ION × 1 CHLORIDE ION × 2 GERANYLGERANYL DIPHOSPHATE × 1 GERAN-8-YL GERAN × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PGTB1_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_id	1n4p
Deposition date deposition_date	2002-11-01
Structure title title	Protein Geranylgeranyltransferase type-I Complexed with Geranylgeranyl Diphosphate
Keywords keywords	protein geranylgeranyltransferase type-I, GGTase, geranylgeranyl, protein prenylation, CaaX, lipid modification, rap2b, TRANSFERASE; TRANSFERASE
Experimental Method method	X-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.

1n4p__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1n4p__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1n4p__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.22 Å
Rg (electron density)	26.32 Å
Total Rg	27.06 Å
Atom count	5388
Residues	660
Excluded volume	95458 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1n4p__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1n4p__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1n4p__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1n4p__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1n4p__assembly_5__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1n4p__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)

Entity 1 Entity 1 polymer

Description description	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Molecular weight formula_weight	44098.1 kDa
EC 编号 ec_number	2.5.1.58,2.5.1.59
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	33443

MAATEGVGESAPGGEPGQPEQPPPPPPPPPAQQPQEEEMAAEAGEAAASPMDDGFLSLDSPTYVLYRDRAEWADIDPVPQNDGPSPVVQIIYSEKFRDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLRSLQKDLQEEMNYIIAIIEEQPKNYQVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVRNNSVWNQRHFVISNTTGYSDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSRYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQSKHSRESDIPASV

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Geranylgeranyl transferase type-1 subunit beta
Molecular weight formula_weight	42466.2 kDa
EC 编号 ec_number	2.5.1.59
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

MAATEDDRLAGSGEGERLDFLRDRHVRFFQRCLQVLPERYSSLETSRLTIAFFALSGLDMLDSLDVVNKDDIIEWIYSLQVLPTEDRSNLDRCGFRGSSYLGIPFNPSKNPGTAHPYDSGHIAMTYTGLSCLIILGDDLSRVDKEACLAGLRALQLEDGSFCAVPEGSENDMRFVYCASCICYMLNNWSGMDMKKAISYIRRSMSYDNGLAQGAGLESHGGSTFCGIASLCLMGKLEEVFSEKELNRIKRWCIMRQQNGYHGRPNKPVDTCYSFWVGATLKLLKIFQYTNFEKNRNYILSTQDRLVGGFAKWPDSHPDALHAYFGICGLSLMEESGICKVHPALNVSTRTSERLRDLHQSWKTKDSKQCSDNVHISS

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
Molecular weight formula_weight	1280.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N

KKKSKTKCVIL

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 6 Entity 6 non-polymer

Description description	GERANYLGERANYL DIPHOSPHATE
Molecular weight formula_weight	450.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	GERAN-8-YL GERAN
Molecular weight formula_weight	274.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1024

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1n4pa_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.6 — Protein prenylyltransferase
Family Family family	a.118.6.1 — Protein prenylyltransferase

Domain ID domain_id	d1n4pb_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.3 — Protein prenyltransferases

Domain ID domain_id	d1n4pc_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.6 — Protein prenylyltransferase
Family Family family	a.118.6.1 — Protein prenylyltransferase

Domain ID domain_id	d1n4pd_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.3 — Protein prenyltransferases

Domain ID domain_id	d1n4pe_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.6 — Protein prenylyltransferase
Family Family family	a.118.6.1 — Protein prenylyltransferase

Domain ID domain_id	d1n4pf_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.3 — Protein prenyltransferases

Domain ID domain_id	d1n4pg_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.6 — Protein prenylyltransferase
Family Family family	a.118.6.1 — Protein prenylyltransferase

Domain ID domain_id	d1n4ph_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.3 — Protein prenyltransferases

Domain ID domain_id	d1n4pi_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.6 — Protein prenylyltransferase
Family Family family	a.118.6.1 — Protein prenylyltransferase

Domain ID domain_id	d1n4pj_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.3 — Protein prenyltransferases

Domain ID domain_id	d1n4pk_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.6 — Protein prenylyltransferase
Family Family family	a.118.6.1 — Protein prenylyltransferase

Domain ID domain_id	d1n4pl_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.3 — Protein prenyltransferases

CATH v4.4 (12 domains)

Domain ID domain_id	1n4pA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	120 — Protein prenylyltransferase

Domain ID domain_id	1n4pB00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1n4pC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	120 — Protein prenylyltransferase

Domain ID domain_id	1n4pD00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1n4pE00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	120 — Protein prenylyltransferase

Domain ID domain_id	1n4pF00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1n4pG00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	120 — Protein prenylyltransferase

Domain ID domain_id	1n4pH00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1n4pI00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	120 — Protein prenylyltransferase

Domain ID domain_id	1n4pJ00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1n4pK00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	120 — Protein prenylyltransferase

Domain ID domain_id	1n4pL00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	272.338 Å
Unit-cell length b length_b	271.566 Å
Unit-cell length c length_c	185.425 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	131.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	29.920 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2280

Protein Geranylgeranyltransferase type-I Complexed with Geranylgeranyl Diphosphate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Geranylgeranyl transferase type-1 subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1n4p__assembly_2__model_1

1n4p__assembly_2__model_1 | I(q)

1n4p__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Protein Geranylgeranyltransferase type-I Complexed with Geranylgeranyl Diphosphate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Geranylgeranyl transferase type-1 subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1n4p__assembly_2__model_1

1n4p__assembly_2__model_1 | I(q)

1n4p__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)