Research workbench
Structure of the monomeric outer membrane porin ompg in the open and closed conformation
Analyse Structure of the monomeric outer membrane porin ompg in the open and closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IWV
- Type
- protein
- Length
- 1,108 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein G
- UniProt
- P76045
- Ligands
- TAM, CA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 70% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Outer membrane protein G | protein | 277 | 1% helix, 70% strand | P76045 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains B
- CA · Calcium ion · metal · 33 copies · chains A, B, C, D
- LDA · Lauryl dimethylamine-N-oxide · additive · 152 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.77 | 0.79 | 90 | CA, LDA |
| 2 | 1090 | 0.74 | 0.77 | 89 | CA, LDA |
| 3 | 1027 | 0.74 | 0.77 | 72 | LDA |
| 4 | 1062 | 0.74 | 0.77 | 80 | CA, LDA |
| 5 | 1008 | 0.74 | 0.77 | 85 | CA, TAM, LDA |
Interfaces
4 interfaces between chains.
- A–D · 542 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 459 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 458 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 270 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2IWV · Structure of the monomeric outer membrane porin OmpG in the open and closed conformation · the same entry in another collection · chain A against A, TM-score 1.00
- P76045 · AlphaFold monomer V2.0 prediction for outer membrane porin G (P76045) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P76045
- Elsewhere: RCSB PDB 2IWV · PDBe 2IWV · UniProt P76045
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