Research workbench
Crystal structure of E. COLI ompf porin in complex with ampicillin
Analyse Crystal structure of E. COLI ompf porin in complex with ampicillin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GCP
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein F
- UniProt
- P02931
- Ligands
- AIC
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer membrane protein F | protein | 333 | 5% helix, 62% strand | P02931 |
Ligands and binding sites
- AIC · (2S,5R,6R)-6-{[(2R)-2-amino-2-phenylethanoyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid · ligand · 2 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 | 930 | 0.70 | 0.75 | 69 | AIC |
| 2 | 614 | 0.68 | 0.77 | 59 | AIC |
| 3 | 255 | 0.48 | 0.74 | 40 | empty |
| 4 | 168 | 0.46 | 0.75 | 35 | empty |
| 5 | 112 | 0.45 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 591 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GCP · Crystal Structure of E. coli OmpF porin in complex with Ampicillin · the same entry in another collection · chain A against A, TM-score 1.00
- P02931 · AlphaFold monomer V2.0 prediction for outer membrane porin F (P02931) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P02931
- Elsewhere: RCSB PDB 4GCP · PDBe 4GCP · UniProt P02931
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