MolNFT v1 · #67379 · protein
Crystallographic analysis of bacterial signal peptidase in ternary complex with arylomycin A2 and a beta-sultam inhibitor
3IIQ: “Crystallographic analysis of bacterial signal peptidase in ternary complex with arylomycin A2 and a…”. X-ray diffraction, 4 ligands (JZA, TRT, CCN), 7 pockets (best druggability 0.63). MolNFT v1 #67379 on GenesisL1: 3D structure…
- PDB
- 3IIQ
- Type
- protein
- Length
- 453 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
- JZA, TRT, CCN, M12
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal peptidase I (EC 3.4.21.89) | protein | 217 | 6% helix, 45% strand | P00803 |
| B | Signal peptidase I (EC 3.4.21.89) | protein | 224 | 6% helix, 46% strand | P00803 |
| C, D | Arylomycin A2 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- JZA · 4-[(1,1-dioxido-1,2-thiazetidin-2-yl)carbonyl]morpholine · ligand · 2 copies · chains A, C, B, D
- TRT · Fragment of triton X-100 · ligand · 2 copies · chains A, B
- CCN · Acetonitrile · ligand · 2 copies · chains A
- M12 · 10-methylundecanoic acid · ligand · 2 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.63 | 0.79 | 51 | empty |
| 2 | 436 | 0.59 | 0.75 | 42 | GOL, CCN |
| 3 | 50 | 0.43 | 0.83 | 11 | empty |
| 4 | 59 | 0.34 | 0.77 | 14 | empty |
| 5 | 50 | 0.28 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 455 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 454 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 451 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent, 2 d-amino, 2 disulfide (nonstandard, covalent ligand, D-amino acid, disulfide).
Compared structures
- 3IIQ · Crystallographic analysis of bacterial signal peptidase in ternary complex with… · 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 A 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 P00803
- Elsewhere: RCSB PDB 3IIQ · PDBe 3IIQ · UniProt P00803
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