MolNFT v1 · #126649 · protein
Staphylococcus capitis divalent metal ion transporter (dmt) in complex with manganese
5M95 · Divalent metal cation transporter mnth: “Staphylococcus capitis divalent metal ion transporter (dmt) in complex with manganese”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.71). MolNFT v1 #126649 on GenesisL1…
- PDB
- 5M95
- Type
- protein
- Length
- 1,030 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Divalent metal cation transporter mnth; Camelid antibody fragment, nanobody
- UniProt
- A0A0S4MEX1
- Ligands
- MN
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Divalent metal cation transporter mnth | protein | 395 | 72% helix, 0% strand | A0A0S4MEX1 |
| B, D | Camelid antibody fragment, nanobody | protein | 120 | 3% helix, 57% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.71 | 0.88 | 46 | empty |
| 2 | 752 | 0.69 | 0.76 | 66 | empty |
| 3 | 644 | 0.69 | 0.76 | 54 | empty |
| 4 | 137 | 0.65 | 0.86 | 21 | empty |
| 5 | 140 | 0.63 | 0.85 | 22 | empty |
Interfaces
4 interfaces between chains.
- D–C · 843 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 828 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 610 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 504 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5M95 · Staphylococcus capitis divalent metal ion transporter (dmt) in complex with manganese · 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 A0A0S4MEX1
- Elsewhere: RCSB PDB 5M95 · PDBe 5M95 · UniProt A0A0S4MEX1
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