MolNFT v1 · #22511 · protein
Crystal structure of escherichia COLI type I signal peptidase in complex with a lipopeptide inhibitor
1T7D: “Crystal structure of escherichia COLI type I signal peptidase in complex with a lipopeptide inhibitor”. X-ray diffraction, 1 ligand (M12), 1 pocket (best druggability 0.47). MolNFT v1 #22511 on GenesisL1: 3D structure, binding sites…
- PDB
- 1T7D
- Type
- protein
- Length
- 443 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal peptidase I; Arylomycin A2
- EC
- 3.4.21.89
- UniProt
- P00803
- Ligands
- M12
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal peptidase I (EC 3.4.21.89) | protein | 208 | 6% helix, 47% strand | P00803 |
| B | Signal peptidase I (EC 3.4.21.89) | protein | 223 | 6% helix, 43% strand | P00803 |
| C, D | Arylomycin A2 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- M12 · 10-methylundecanoic acid · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.47 | 0.85 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–C · 430 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 417 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 60 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent, 2 d-amino, 1 disulfide (nonstandard, covalent ligand, D-amino acid, disulfide).
Compared structures
- 1T7D · Crystal structure of Escherichia coli type I signal peptidase in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P00803 · AlphaFold monomer V2.0 prediction for signal peptidase I (P00803) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P00803
- Elsewhere: RCSB PDB 1T7D · PDBe 1T7D · UniProt P00803
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