MolNFT v1 · #40919 · protein
Gmppnp-stabilized ng domain complex of the srp gtpases ffh and ftsy
2J7P · Signal recognition particle protein: “Gmppnp-stabilized ng domain complex of the srp gtpases ffh and ftsy”. X-ray diffraction, 4 ligands (GNP, MG, K), 15 pockets (best druggability 0.82). MolNFT v1 #40919 on GenesisL1: 3D structure…
- PDB
- 2J7P
- Type
- protein
- Length
- 1,107 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle protein; Cell division protein ftsy
- UniProt
- O07347, P83749
- Ligands
- GNP, MG, K, IOD
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle protein | protein | 292 | 48% helix, 14% strand | O07347 |
| B | Signal recognition particle protein | protein | 291 | 48% helix, 14% strand | O07347 |
| D | Cell division protein ftsy | protein | 265 | 48% helix, 14% strand | P83749 |
| E | Cell division protein ftsy | protein | 259 | 49% helix, 14% strand | P83749 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, D, B, E
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, E
- K · Potassium ion · metal · 2 copies · chains D, E
- IOD · Iodide ion · ion · 16 copies · chains A, B, E, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.82 | 0.89 | 65 | EDO, GNP, MG |
| 2 | 550 | 0.82 | 0.88 | 82 | GNP, MG |
| 3 | 806 | 0.77 | 0.81 | 76 | IOD |
| 4 | 55 | 0.71 | 0.98 | 24 | EDO |
| 5 | 285 | 0.58 | 0.78 | 52 | IOD |
Interfaces
4 interfaces between chains.
- B–E · 1589 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1582 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 478 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 352 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2J7P · GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY · the same entry in another collection · chain E against E, TM-score 1.00
- P83749 · AlphaFold monomer V2.0 prediction for signal recognition particle receptor ftsy (P83749) · a predicted model of the same protein · chain E against A, TM-score 0.95
- O07347 · AlphaFold monomer V2.0 prediction for signal recognition particle protein (O07347) · 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 O07347
- Every structure of UniProt P83749
- Elsewhere: RCSB PDB 2J7P · PDBe 2J7P · UniProt O07347 · UniProt P83749
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