MolNFT v1 · #27832 · protein
The three-dimensional structure of mntc from synechocystis 6803
1XVL · Mn transporter: “The three-dimensional structure of mntc from synechocystis 6803”. X-ray diffraction, 1 ligand (MN), 7 pockets (best druggability 0.69). MolNFT v1 #27832 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XVL
- Type
- protein
- Length
- 767 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mn transporter
- UniProt
- Q79EF9
- Ligands
- MN
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mn transporter | protein | 279 | 42% helix, 14% strand | Q79EF9 |
| B | Mn transporter | protein | 271 | 44% helix, 15% strand | Q79EF9 |
| C | Mn transporter | protein | 217 | 42% helix, 8% strand | Q79EF9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.69 | 0.82 | 47 | empty |
| 2 | 450 | 0.60 | 0.75 | 47 | empty |
| 3 | 191 | 0.55 | 0.79 | 31 | empty |
| 4 | 110 | 0.41 | 0.77 | 22 | empty |
| 5 | 100 | 0.40 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 864 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 300 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1XVL · The three-dimensional structure of MntC from Synechocystis 6803 · 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 Q79EF9
- Elsewhere: RCSB PDB 1XVL · PDBe 1XVL · UniProt Q79EF9
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