MolNFT v1 · #6003 · protein
Crystal structure of human squalene synthase
1EZF · Farnesyl-diphosphate farnesyltransferase: “Crystal structure of human squalene synthase”. X-ray diffraction, 1 ligand (IN0), 7 pockets (best druggability 0.79). MolNFT v1 #6003 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1EZF
- Type
- protein
- Length
- 967 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl-diphosphate farnesyltransferase
- EC
- 2.5.1.21
- UniProt
- P37268
- Ligands
- IN0
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl-diphosphate farnesyltransferase (EC 2.5.1.21) | protein | 323 | 73% helix, 0% strand | P37268 |
| B | Farnesyl-diphosphate farnesyltransferase (EC 2.5.1.21) | protein | 324 | 72% helix, 0% strand | P37268 |
| C | Farnesyl-diphosphate farnesyltransferase (EC 2.5.1.21) | protein | 320 | 73% helix, 0% strand | P37268 |
Ligands and binding sites
- IN0 · N-{2-[trans-7-chloro-1-(2,2-dimethyl-propyl) -5-naphthalen-1-yl-2-oxo-1,2,3,5-tetrahydro-benzo[e] [1,4]oxazepin-3-yl]-acetyl}-aspartic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.79 | 0.81 | 61 | IN0 |
| 2 | 977 | 0.79 | 0.80 | 73 | IN0 |
| 3 | 873 | 0.76 | 0.80 | 65 | IN0 |
| 4 | 135 | 0.51 | 0.80 | 15 | empty |
| 5 | 74 | 0.44 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 768 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 711 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 663 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P37268
- Elsewhere: RCSB PDB 1EZF · PDBe 1EZF · UniProt P37268
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