MolNFT v1 · #125261 · protein
Structure of the GTPase heterodimer of chloroplast SRP54 and ftsy from arabidopsis thaliana
5L3R · Signal recognition particle 54 kda protein, chloroplastic: “Structure of the GTPase heterodimer of chloroplast SRP54 and ftsy from arabidopsis thaliana”. X-ray diffraction, 2 ligands (GCP, MG), 9 pockets (best druggability 0.87).…
- PDB
- 5L3R
- Type
- protein
- Length
- 1,115 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle 54 kda protein, chloroplastic; Cell division protein ftsy…
- UniProt
- P37107, O80842
- Ligands
- GCP, MG
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle 54 kda protein, chloroplastic | protein | 267 | 48% helix, 15% strand | P37107 |
| B | Cell division protein ftsy homolog, chloroplastic | protein | 290 | 48% helix, 13% strand | O80842 |
| C | Signal recognition particle 54 kda protein, chloroplastic | protein | 269 | 49% helix, 15% strand | P37107 |
| D | Cell division protein ftsy homolog, chloroplastic | protein | 289 | 48% helix, 15% strand | O80842 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.87 | 0.88 | 133 | GCP, MG |
| 2 | 185 | 0.54 | 0.79 | 30 | empty |
| 3 | 114 | 0.47 | 0.79 | 22 | empty |
| 4 | 113 | 0.44 | 0.78 | 21 | empty |
| 5 | 153 | 0.44 | 0.75 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1605 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1582 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 225 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 210 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 121 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5L3R · Structure of the GTPase heterodimer of chloroplast SRP54 and FtsY from Arabidopsis… · the same entry in another collection · chain D against D, TM-score 1.00
- P37107 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein… · a predicted model of the same protein · chain A against A, TM-score 0.96
- O80842 · AlphaFold monomer V2.0 prediction for cell division protein ftsy homolog, chloroplastic… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P37107
- Every structure of UniProt O80842
- Elsewhere: RCSB PDB 5L3R · PDBe 5L3R · UniProt P37107 · UniProt O80842
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