MolNFT v1 · #38259 · protein
Crystal structure of tonb in complex with fhua, E. COLI outer membrane receptor for ferrichrome
2GRX · Ferrichrome-iron receptor: “Crystal structure of tonb in complex with fhua, E. COLI outer membrane receptor for ferrichrome”. X-ray diffraction, 10 ligands (FTT, GCN, DPO), 14 pockets (best druggability 0.83). MolNFT v1 #38259 on…
- 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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