MolNFT v1 · #149522 · protein
Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate
6G31 · Geranylgeranyl pyrophosphate synthase: “Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate”. X-ray diffraction, 2 ligands (ZOL, MG), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6G31
- Type
- protein
- Length
- 3,347 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthase
- EC
- 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10
- UniProt
- O95749
- Ligands
- ZOL, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 11 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 286 | 74% helix, 1% strand | O95749 |
| B | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 284 | 76% helix, 1% strand | O95749 |
| C | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 288 | 74% helix, 1% strand | O95749 |
| D | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 280 | 76% helix, 1% strand | O95749 |
| E | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 249 | 66% helix, 2% strand | O95749 |
| F, J | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 285 | 77% helix, 1% strand | O95749 |
| G | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 281 | 76% helix, 1% strand | O95749 |
| H | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 281 | 78% helix, 1% strand | O95749 |
| I | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 276 | 74% helix, 1% strand | O95749 |
| K | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 269 | 76% helix, 1% strand | O95749 |
| L | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.-, 2.5.1.1, 2.5.1.29, 2.5.1.10) | protein | 283 | 77% helix, 1% strand | O95749 |
Ligands and binding sites
- ZOL · Zoledronic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 36 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.83 | 0.84 | 111 | ZOL, MG |
| 2 | 955 | 0.81 | 0.83 | 136 | ZOL, MG |
| 3 | 1200 | 0.80 | 0.82 | 109 | ZOL, MG |
| 4 | 1137 | 0.79 | 0.81 | 111 | ZOL, MG |
| 5 | 937 | 0.79 | 0.81 | 86 | ZOL, MG |
Interfaces
21 interfaces between chains.
- A–B · 1627 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1610 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 1514 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 1508 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1480 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6G31 · Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to… · the same entry in another collection · chain L against L, TM-score 1.00
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 O95749
- Elsewhere: RCSB PDB 6G31 · PDBe 6G31 · UniProt O95749
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