8rdx

PGGtase I in complex with probe BAY-6092

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 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） ZINC ION × 1 CHLORIDE ION × 1 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） ZINC ION × 1 CHLORIDE ION × 1 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） ZINC ION × 1 CHLORIDE ION × 1 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） ZINC ION × 1 CHLORIDE ION × 1 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Geranylgeranyl transferase type-1 subunit beta × 1 （P53610） ZINC ION × 1 CHLORIDE ION × 1 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	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 1–314； UniProt 55–368 Author chain C； PDBConstruct 1–314； UniProt 55–368 Author chain E； PDBConstruct 1–314； UniProt 55–368 Author chain G； PDBConstruct 1–314； UniProt 55–368 Author chain I； PDBConstruct 1–314； UniProt 55–368 Author chain K； PDBConstruct 1–314； UniProt 55–368

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 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha × 1 （Q04631） ZINC ION × 1 CHLORIDE ION × 1 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	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 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha × 1 （Q04631） ZINC ION × 1 CHLORIDE ION × 1 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha × 1 （Q04631） ZINC ION × 1 CHLORIDE ION × 1 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha × 1 （Q04631） ZINC ION × 1 CHLORIDE ION × 1 DIPHOSPHATE × 1 (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one × 1 water × 1	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 1–346； UniProt 18–363 Author chain D； PDBConstruct 1–346； UniProt 18–363 Author chain F； PDBConstruct 1–346； UniProt 18–363 Author chain H； PDBConstruct 1–346； UniProt 18–363 Author chain J； PDBConstruct 1–346； UniProt 18–363 Author chain L； PDBConstruct 1–346； UniProt 18–363

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	8rdx
Deposition date deposition_date	2023-12-08
Structure title title	PGGtase I in complex with probe BAY-6092
Keywords keywords	inhibitor, 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.

8rdx__assembly_1__model_1

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

Download this curve (.dat)

8rdx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rdx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.01 Å
Rg (electron density)	26.16 Å
Total Rg	26.91 Å
Atom count	5372
Residues	660
Excluded volume	95033 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rdx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8rdx__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8rdx__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`8rdx__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`8rdx__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`8rdx__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 (7)

Entity 1 Entity 1 polymer

Description description	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Molecular weight formula_weight	37871.6 kDa
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	32241

FLSLDSPTYVLYRDRAEWADIDPVPQNDGPSPVVQIIYSEKFRDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLRSLQKDLQEEMNYIIAIIEEQPKNYQVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVRNNSVWNQRHFVISNTTGYSDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSRYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQSKHS

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Spodoptera

Entity 2 Entity 2 polymer

Description description	Geranylgeranyl transferase type-1 subunit beta
Molecular weight formula_weight	39184.7 kDa
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

LDFLRDRHVRFFQRCLQVLPERYSSLETSRLTIAFFALSGLDMLDSLDVVNKDDIIEWIYSLQVLPTEDRSNLDRCGFRGSSYLGIPFNPSKNPGTAHPYDSGHIAMTYTGLSCLIILGDDLSRVDKEACLAGLRALQLEDGSFCAVPEGSENDMRFVYCASCICYMLNNWSGMDMKKAISYIRRSMSYDNGLAQGAGLESHGGSTFCGIASLCLMGKLEEVFSEKELNRIKRWCIMRQQNGYHGRPNKPVDTCYSFWVGATLKLLKIFQYTNFEKNRNYILSTQDRLVGGFAKWPDSHPDALHAYFGICGLSLMEESGICKVHPALNVSTRTSERLRDLHQSWKT

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Spodoptera

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	DIPHOSPHATE
Molecular weight formula_weight	173.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	(5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one
Molecular weight formula_weight	490.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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Unit-cell length a length_a	270.891 Å
Unit-cell length b length_b	269.263 Å
Unit-cell length c length_c	185.248 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	131.77 °
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	3.670 Å
Low-resolution limit resolution_low	48.210 Å
R factor r_factor	0.1382
R_work r_work	0.1371
R_free r_free	0.1891

PGGtase I in complex with probe BAY-6092

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

8rdx__assembly_1__model_1

8rdx__assembly_1__model_1 | I(q)

8rdx__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (2)

PGGtase I in complex with probe BAY-6092

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

8rdx__assembly_1__model_1

8rdx__assembly_1__model_1 | I(q)

8rdx__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (2)