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1TNZ:
Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a RRCVLL Peptide Derived from Cdc42 splice isoform-2
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PDB ID:
1TNZ
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MMDB ID:
29952
PDB Deposition Date:
2004/6/11
Updated in MMDB:
2004/12
Experimental Method:
x-ray diffraction
Resolution:
2.9 Å
Source Organism:
synthetic construct
▼
Taxonomy
Molecule
synthetic construct
M, N, O, P, Q, R
Rattus norvegicus
A, B, C, D, E, F, G, H, I, J, K, L
Similar Structures:
VAST+
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Default Biological Unit
All Biological Units (6)
Asymmetric Unit
Biological Unit for 1TNZ: trimeric; determined by author and by software (PISA)
Molecular Graphic
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Interactions
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A
A: geranylgeranyltransferase type I alpha subunit
B
B: Geranylgeranyl transferase type I beta subunit
M
M: Cell division control protein 42 homolog (Cdc42)
1
ZN: ZINC ION
2
MGM: 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE
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Protein
Nucleotide
Chemical
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Format:
ASN.1 (Cn3D)
PDB
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PNG (image)
Data Set:
alpha-Carbons
Single 3D structure
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Molecular Components in 1TNZ
Label
Count
Molecule
Proteins (3 molecules)
A
1
Geranylgeranyltransferase Type I Alpha Subunit
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 167-179
helix 185-193
helix 200-213
helix 219-229
helix 234-246
helix 253-269
helix 274-284
helix 293-302
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 (217-288): click to see VAST similar structures
3
Domain 4 (289-377): click to see VAST similar structures
4
PLN02789 superfamily
cl33568(64-365): farnesyltranstransferase
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B
1
Geranylgeranyl Transferase Type I Beta Subunit
1 Protein
SS Diagram
Features
Domain Families
Specific Hits
Super Families
1
75
150
225
300
377
377 residues, click to see VAST similar structures.
helix 22-33
helix 47-61
helix 69-78
helix 122-135
helix 144-153
helix 173-185
helix 193-202
helix 220-233
helix 242-254
helix 274-283
helix 292-301
helix 319-330
helix 348-361
strand 79-82
strand 93-96
strand 154-157
strand 159-162
strand 203-206
strand 208-211
strand 340-343
strand 344-347
active site cavity
active site(23)
location: 42, residue: S
location: 45, residue: T
location: 46, residue: S
location: 49, residue: T
location: 53, residue: F
location: 121, residue: H
location: 123, residue: A
location: 124, residue: M
location: 126, residue: Y
location: 127, residue: T
location: 173, residue: R
location: 176, residue: Y
location: 177, residue: C
location: 219, residue: H
location: 221, residue: G
location: 225, residue: C
location: 269, residue: D
location: 271, residue: C
location: 272, residue: Y
location: 275, residue: W
location: 311, residue: K
location: 320, residue: L
location: 321, residue: H
Zn2+ binding site
Zn2+ binding site(3)
location: 269, residue: D
location: 271, residue: C
location: 321, residue: H
lipid binding pocket
lipid(12)
location: 49, residue: T
location: 52, residue: F
location: 173, residue: R
location: 176, residue: Y
location: 219, residue: H
location: 221, residue: G
location: 225, residue: C
location: 263, residue: R
location: 266, residue: K
location: 272, residue: Y
location: 275, residue: W
location: 320, residue: L
peptide binding pocket
peptide(8)
location: 45, residue: T
location: 46, residue: S
location: 49, residue: T
location: 123, residue: A
location: 124, residue: M
location: 173, residue: R
location: 269, residue: D
location: 311, residue: K
heterodimer interface
heterodimer interface(12)
location: 168, residue: S
location: 206, residue: Y
location: 216, residue: L
location: 217, residue: E
location: 222, residue: S
location: 250, residue: R
location: 253, residue: I
location: 255, residue: R
location: 256, residue: Q
location: 263, residue: R
location: 264, residue: P
location: 265, residue: N
GGTase-I
cd02895 (22-332): Geranylgeranyltransferase types I (GGTase-I)-like proteins containing the protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold)
ISOPREN_C2_like superfamily
cl08267(22-332): This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2...
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M
1
Cell Division Control Protein 42 Homolog (Cdc42)
1 Protein
1
6
6 residues, click to see VAST similar structures.
Chemicals and Non-standard biopolymers (2 molecules)
1
1
ZINC ION
2
1
2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE
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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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