Research workbench
Crystal structure of ipgc in complex with the chaperone binding region of ipab
Analyse Crystal structure of ipgc in complex with the chaperone binding region of ipab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GZ1
- Type
- protein
- Length
- 309 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein ipgc; Invasin ipab
- UniProt
- P0A2U4, P18011
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein ipgc | protein | 144 | 75% helix, 0% strand | P0A2U4 |
| B | Chaperone protein ipgc | protein | 142 | 76% helix, 0% strand | P0A2U4 |
| P | Invasin ipab | protein | 13 | 0% helix, 0% strand | P18011 |
| Q | Invasin ipab | protein | 10 | 0% helix, 0% strand | P18011 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, Q, B, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.63 | 0.84 | 24 | empty |
| 2 | 234 | 0.56 | 0.78 | 39 | empty |
| 3 | 120 | 0.48 | 0.79 | 25 | empty |
| 4 | 57 | 0.36 | 0.79 | 14 | GOL |
| 5 | 67 | 0.30 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1430 Ų buried · 6 hydrogen bonds · protein-protein
- B–P · 628 Ų buried · 5 hydrogen bonds · protein-protein
- A–Q · 573 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3GZ1 · Crystal structure of IpgC in complex with the chaperone binding region of IpaB · the same entry in another collection · chain Q against Q, TM-score 1.00
- P0A2U4 · AlphaFold monomer V2.0 prediction for chaperone protein ipgc (P0A2U4) · a predicted model of the same protein · chain B against A, TM-score 0.91
- P18011 · AlphaFold monomer V2.0 prediction for invasin ipab (P18011) · a predicted model of the same protein · chain Q against A, TM-score 0.40
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 P0A2U4
- Every structure of UniProt P18011
- Elsewhere: RCSB PDB 3GZ1 · PDBe 3GZ1 · UniProt P0A2U4 · UniProt P18011
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