Research workbench
Crystal structure of tonb in complex with fhua, E. COLI outer membrane receptor for ferrichrome
Analyse Crystal structure of tonb in complex with fhua, E. COLI outer membrane receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GRX
- Type
- protein
- Length
- 1,549 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferrichrome-iron receptor; Protein tonb
- UniProt
- P06971, P94739
- Ligands
- FTT, GCN, DPO, DAO, EAP, FCI, MYR, KDO, GMH, PO4
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferrichrome-iron receptor | protein | 702 | 4% helix, 52% strand | P06971 |
| B | Ferrichrome-iron receptor | protein | 691 | 4% helix, 52% strand | P06971 |
| C, D | Protein tonb | protein | 78 | 17% helix, 22% strand | P94739 |
Ligands and binding sites
- FTT · 3-hydroxy-tetradecanoic acid · ligand · 8 copies · chains A, B
- GCN · 2-amino-2,3-dideoxy-alpha-D-glucoyranose · ligand · 4 copies · chains A, B
- DPO · Diphosphate · ligand · 2 copies · chains A, B
- DAO · Lauric acid · ligand · 2 copies · chains A, B
- EAP · 2-amino-vinyl-phosphate · ligand · 2 copies · chains B, A
- FCI · Ferricrocin-iron · ligand · 2 copies · chains A, B
- MYR · Myristic acid · ligand · chains B
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 4 copies · chains A, B
- GMH · L-glycero-alpha-D-manno-heptopyranose · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.83 | 0.96 | 57 | empty |
| 2 | 1156 | 0.81 | 0.83 | 98 | empty |
| 3 | 1184 | 0.80 | 0.82 | 84 | empty |
| 4 | 163 | 0.80 | 0.96 | 43 | empty |
| 5 | 993 | 0.79 | 0.81 | 99 | FCI |
Interfaces
3 interfaces between chains.
- A–C · 1359 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 657 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2GRX · Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for… · the same entry in another collection · chain A against A, TM-score 1.00
- P06971 · AlphaFold monomer V2.0 prediction for ferrichrome outer membrane TRANSPORTER/PHAGE… · a predicted model of the same protein · chain B 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 P06971
- Every structure of UniProt P94739
- Elsewhere: RCSB PDB 2GRX · PDBe 2GRX · UniProt P06971 · UniProt P94739
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