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3DPY:
Protein farnesyltransferase complexed with FPP and caged TKCVIM substrate
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PDB ID:
3DPY
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MMDB ID:
67041
PDB Deposition Date:
2008/7/9
Updated in MMDB:
2008/10
Experimental Method:
x-ray diffraction
Resolution:
2.7 Å
Source Organism:
synthetic construct
▼
Taxonomy
Molecule
synthetic construct
C
Rattus norvegicus
A, B
Similar Structures:
VAST+
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Biological Unit
Asymmetric Unit
Biological Unit for 3DPY: trimeric; determined by author and by software (PISA)
Molecular Graphic
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Interactions
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A
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B
B: Protein farnesyltransferase subunit beta
C
C: caged substrate
1
ZN: ZINC ION
2
FPP: FARNESYL DIPHOSPHATE
3
ACY: ACETIC ACID
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Nucleotide
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Format:
ASN.1 (Cn3D)
PDB
XML
JSON
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Data Set:
alpha-Carbons
Single 3D structure
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Molecular Components in 3DPY
Label
Count
Molecule
Proteins (3 molecules)
A
1
Protein Farnesyltransferase/geranylgeranyltransferase Type-1 Subunit Alpha
1 Protein
SS Diagram
3D Domains
Domain Families
Super Families
1
75
150
225
300
377
377 residues, click to see VAST similar structures.
helix 94-109
helix 114-126
helix 131-144
helix 148-161
helix 168-179
helix 185-195
helix 200-213
helix 219-229
helix 234-246
helix 253-269
helix 275-284
helix 294-302
helix 309-325
helix 330-346
helix 353-366
Domain 1 (1-146): click to see VAST similar structures
1
Domain 2 (147-216): click to see VAST similar structures
2
Domain 3 (217-289): click to see VAST similar structures
3
Domain 4 (290-377): click to see VAST similar structures
4
PLN02789 superfamily
cl33568(64-365): farnesyltranstransferase
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B
1
Protein Farnesyltransferase Subunit Beta
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
1
75
150
225
300
375
437
437 residues, click to see VAST similar structures.
helix 43-60
helix 75-86
helix 100-114
helix 120-133
helix 151-163
helix 174-183
helix 202-214
helix 249-262
helix 270-279
helix 308-318
helix 332-341
helix 360-373
helix 405-415
strand 184-187
strand 189-192
strand 232-235
strand 237-240
strand 343-346
strand 348-351
strand 374-379
strand 380-385
Domain 1 (68-168): click to see VAST similar structures
1
Domain 2 (169-325): click to see VAST similar structures
2
Domain 1 (326-395): click to see VAST similar structures
1
Domain 2 (396-437): click to see VAST similar structures
2
active site cavity
active site(23)
location: 95, residue: C
location: 98, residue: A
location: 99, residue: S
location: 102, residue: W
location: 106, residue: W
location: 149, residue: H
location: 151, residue: A
location: 152, residue: P
location: 154, residue: Y
location: 155, residue: A
location: 202, residue: R
location: 205, residue: Y
location: 206, residue: C
location: 248, residue: H
location: 250, residue: G
location: 254, residue: C
location: 297, residue: D
location: 299, residue: C
location: 300, residue: Y
location: 303, residue: W
location: 352, residue: D
location: 361, residue: Y
location: 362, residue: H
Zn2+ binding site
Zn2+ binding site(3)
location: 297, residue: D
location: 299, residue: C
location: 362, residue: H
lipid binding pocket
lipid binding(12)
location: 102, residue: W
location: 105, residue: Y
location: 202, residue: R
location: 205, residue: Y
location: 248, residue: H
location: 250, residue: G
location: 254, residue: C
location: 291, residue: R
location: 294, residue: K
location: 300, residue: Y
location: 303, residue: W
location: 361, residue: Y
peptide binding pocket
peptide(8)
location: 98, residue: A
location: 99, residue: S
location: 102, residue: W
location: 151, residue: A
location: 152, residue: P
location: 202, residue: R
location: 297, residue: D
location: 352, residue: D
heterodimer interface
heterodimer interface(12)
location: 197, residue: G
location: 235, residue: W
location: 245, residue: M
location: 246, residue: E
location: 251, residue: Y
location: 275, residue: Q
location: 278, residue: T
location: 280, residue: R
location: 281, residue: Q
location: 291, residue: R
location: 292, residue: C
location: 293, residue: N
FTase
cd02893 (75-373): Protein farnesyltransferase (FTase)_like proteins containing the protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold)
ISOPREN_C2_like superfamily
cl08267(75-373): This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2...
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C
1
Caged Substrate
1 Protein
1
6
6 residues, click to see VAST similar structures.
Chemicals and Non-standard biopolymers (3 molecules)
1
1
ZINC ION
2
1
FARNESYL DIPHOSPHATE
3
1
ACETIC ACID
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Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH.
"
MMDB and VAST+: tracking structural similarities between macromolecular complexes.
Nucleic Acids Res. 2014 Jan; 42(Database issue)
:D297-303
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