Research workbench
Crystal structure of the deinococcus radiodurans NRAMP/MNTH divalent transition metal transporter in the outward-open, manganese-bound conformation
Analyse Crystal structure of the deinococcus radiodurans NRAMP/MNTH divalent transition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BU5
- Type
- protein
- Length
- 398 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Divalent metal cation transporter mnth
- UniProt
- Q9RTP8
- Ligands
- SPD, MN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Divalent metal cation transporter mnth | protein | 398 | 81% helix, 0% strand | Q9RTP8 |
Ligands and binding sites
- SPD · Spermidine · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 10 copies · chains A
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 | 99 | 0.74 | 0.96 | 31 | empty |
| 2 | 326 | 0.65 | 0.80 | 33 | SPD |
| 3 | 119 | 0.44 | 0.77 | 19 | empty |
| 4 | 99 | 0.39 | 0.75 | 18 | empty |
| 5 | 56 | 0.31 | 0.75 | 13 | empty |
Compared structures
- Q9RTP8 · AlphaFold monomer V2.0 prediction for divalent metal cation transporter mnth (Q9RTP8) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9RTP8
- Elsewhere: RCSB PDB 6BU5 · PDBe 6BU5 · UniProt Q9RTP8
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