MolNFT v1 · #58689 · protein
Crystal structure of TOC34 from pisum sativum in complex with MG2+ and gmppnp
3BB1 · Translocase of chloroplast 34: “Crystal structure of TOC34 from pisum sativum in complex with MG2+ and gmppnp”. X-ray diffraction, 2 ligands (GNP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #58689 on GenesisL1: 3D…
- PDB
- 3BB1
- Type
- protein
- Length
- 1,980 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translocase of chloroplast 34
- EC
- 3.6.5.-
- UniProt
- Q41009
- Ligands
- GNP, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translocase of chloroplast 34 (EC 3.6.5.-) | protein | 252 | 39% helix, 20% strand | Q41009 |
| B | Translocase of chloroplast 34 (EC 3.6.5.-) | protein | 243 | 40% helix, 20% strand | Q41009 |
| C | Translocase of chloroplast 34 (EC 3.6.5.-) | protein | 246 | 39% helix, 20% strand | Q41009 |
| D | Translocase of chloroplast 34 (EC 3.6.5.-) | protein | 247 | 39% helix, 19% strand | Q41009 |
| E | Translocase of chloroplast 34 (EC 3.6.5.-) | protein | 248 | 39% helix, 20% strand | Q41009 |
| F | Translocase of chloroplast 34 (EC 3.6.5.-) | protein | 245 | 38% helix, 20% strand | Q41009 |
| G | Translocase of chloroplast 34 (EC 3.6.5.-) | protein | 251 | 38% helix, 18% strand | Q41009 |
| H | Translocase of chloroplast 34 (EC 3.6.5.-) | protein | 248 | 38% helix, 20% strand | Q41009 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 6 copies · chains A, C, E, F, G
- PGE · Triethylene glycol · additive · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.87 | 0.94 | 62 | empty |
| 2 | 789 | 0.87 | 0.90 | 126 | MG, GNP |
| 3 | 399 | 0.86 | 0.94 | 36 | empty |
| 4 | 441 | 0.85 | 0.93 | 35 | empty |
| 5 | 505 | 0.84 | 0.91 | 39 | empty |
Interfaces
15 interfaces between chains.
- G–H · 1312 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1302 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1266 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1258 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 499 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3BB1 · Crystal structure of Toc34 from Pisum sativum in complex with Mg2+ and GMPPNP · the same entry in another collection · chain H against H, TM-score 1.00
- Q41009 · AlphaFold monomer V2.0 prediction for translocase of chloroplast 34 (Q41009) · a predicted model of the same protein · chain F 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 Q41009
- Elsewhere: RCSB PDB 3BB1 · PDBe 3BB1 · UniProt Q41009
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