MolNFT v1 · #100051 · protein
Gggps from methanothermobacter thermautotrophicus
4MM1 · Geranylgeranylglyceryl phosphate synthase: “Gggps from methanothermobacter thermautotrophicus”. X-ray diffraction, 1 ligand (1GP), 13 pockets (best druggability 0.83). MolNFT v1 #100051 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4MM1
- Type
- protein
- Length
- 1,339 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranylglyceryl phosphate synthase
- EC
- 2.5.1.41
- UniProt
- O26652
- Ligands
- 1GP
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 238 | 45% helix, 20% strand | O26652 |
| B | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 215 | 41% helix, 22% strand | O26652 |
| C | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 234 | 41% helix, 21% strand | O26652 |
| D | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 220 | 43% helix, 21% strand | O26652 |
| E | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 225 | 43% helix, 21% strand | O26652 |
| F | Geranylgeranylglyceryl phosphate synthase (EC 2.5.1.41) | protein | 207 | 37% helix, 22% strand | O26652 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.83 | 0.91 | 86 | empty |
| 2 | 189 | 0.80 | 0.95 | 41 | 1GP, PGE |
| 3 | 207 | 0.80 | 0.94 | 50 | 1GP, PGE |
| 4 | 180 | 0.79 | 0.94 | 32 | PGE |
| 5 | 182 | 0.79 | 0.94 | 39 | 1GP, PGE |
Interfaces
12 interfaces between chains.
- C–E · 1179 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 1173 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 1156 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 739 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 732 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4MM1 · GGGPS from Methanothermobacter thermautotrophicus · the same entry in another collection · chain F against F, TM-score 1.00
- O26652 · AlphaFold monomer V2.0 prediction for geranylgeranylglyceryl phosphate synthase (O26652) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O26652
- Elsewhere: RCSB PDB 4MM1 · PDBe 4MM1 · UniProt O26652
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