Research workbench
Crystal structure of an S. thermophilus nfeob E67A mutant bound to GDP
Analyse Crystal structure of an S. thermophilus nfeob E67A mutant bound to GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B1W
- Type
- protein
- Length
- 1,034 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferrous iron uptake transporter protein B
- UniProt
- Q5M586
- Ligands
- GDP
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferrous iron uptake transporter protein B | protein | 262 | 50% helix, 19% strand | Q5M586 |
| B | Ferrous iron uptake transporter protein B | protein | 260 | 49% helix, 16% strand | Q5M586 |
| C | Ferrous iron uptake transporter protein B | protein | 258 | 50% helix, 18% strand | Q5M586 |
| D | Ferrous iron uptake transporter protein B | protein | 254 | 49% helix, 18% strand | Q5M586 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.79 | 0.95 | 19 | empty |
| 2 | 568 | 0.76 | 0.83 | 71 | empty |
| 3 | 549 | 0.68 | 0.78 | 50 | empty |
| 4 | 300 | 0.59 | 0.78 | 44 | empty |
| 5 | 198 | 0.53 | 0.78 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1123 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 976 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 491 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 416 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3B1W · Crystal structure of an S. thermophilus NFeoB E67A mutant bound to GDP · the same entry in another collection · 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 Q5M586
- Elsewhere: RCSB PDB 3B1W · PDBe 3B1W · UniProt Q5M586
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