MolNFT v1 · #58381 · protein
Crystal structure of an S. thermophilus nfeob E67A mutant bound to GDP
3B1W · Ferrous iron uptake transporter protein B: “Crystal structure of an S. thermophilus nfeob E67A mutant bound to GDP”. X-ray diffraction, 1 ligand (GDP), 11 pockets (best druggability 0.79). MolNFT v1 #58381 on GenesisL1: 3D…
- 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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