MolNFT v1 · #125262 · protein
Structure of the GTPase heterodimer of crenarchaeal SRP54 and ftsy
5L3S · Signal recognition particle 54 kda protein: “Structure of the GTPase heterodimer of crenarchaeal SRP54 and ftsy”. X-ray diffraction, 4 ligands (GNP, G, MG), 20 pockets (best druggability 0.82). MolNFT v1 #125262 on GenesisL1: 3D…
- PDB
- 5L3S
- Type
- protein
- Length
- 2,207 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle 54 kda protein; Signal recognition particle receptor ftsy
- UniProt
- Q97ZE7, P27414
- Ligands
- GNP, G, MG, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle 54 kda protein | protein | 274 | 50% helix, 15% strand | Q97ZE7 |
| B | Signal recognition particle receptor ftsy | protein | 283 | 51% helix, 17% strand | P27414 |
| C | Signal recognition particle 54 kda protein | protein | 270 | 50% helix, 16% strand | Q97ZE7 |
| D | Signal recognition particle receptor ftsy | protein | 271 | 50% helix, 15% strand | P27414 |
| E | Signal recognition particle 54 kda protein | protein | 271 | 51% helix, 15% strand | Q97ZE7 |
| F | Signal recognition particle receptor ftsy | protein | 283 | 51% helix, 16% strand | P27414 |
| G | Signal recognition particle 54 kda protein | protein | 277 | 50% helix, 15% strand | Q97ZE7 |
| H | Signal recognition particle receptor ftsy | protein | 278 | 52% helix, 15% strand | P27414 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- G · Guanosine-5'-monophosphate · ligand · 4 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
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, G, C, E, F, H
- GOL · Glycerol · additive · 18 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.82 | 0.89 | 71 | GNP, MG, GOL |
| 2 | 440 | 0.81 | 0.89 | 66 | GNP, MG, GOL |
| 3 | 532 | 0.80 | 0.87 | 76 | GNP, MG, GOL |
| 4 | 649 | 0.79 | 0.85 | 84 | GNP, MG, GOL |
| 5 | 841 | 0.74 | 0.78 | 75 | G |
Interfaces
14 interfaces between chains.
- E–F · 1563 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1560 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1559 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1559 Ų buried · 25 hydrogen bonds · protein-protein
- A–G · 853 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5L3S · Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY · the same entry in another collection · chain H against H, TM-score 1.00
- Q97ZE7 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (Q97ZE7) · a predicted model of the same protein · chain G against A, TM-score 0.84
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 Q97ZE7
- Every structure of UniProt P27414
- Elsewhere: RCSB PDB 5L3S · PDBe 5L3S · UniProt Q97ZE7 · UniProt P27414
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