MolNFT v1 · #126648 · protein
Crystal structure of staphylococcus capitis divalent metal ion transporter (dmt) in complex with nanobody
5M94 · Divalent metal cation transporter mnth: “Crystal structure of staphylococcus capitis divalent metal ion transporter (dmt) in complex with nanobody”. X-ray diffraction, 19 pockets (best druggability 0.70). MolNFT v1 #126648 on…
- PDB
- 5M94
- Type
- protein
- Length
- 1,042 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
- Pockets
- 19 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Divalent metal cation transporter mnth | protein | 401 | 81% helix, 0% strand | A0A0S4MEX1 |
| B, D | Camelid antibody fragment, nanobody | protein | 120 | 3% helix, 54% strand | — |
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.70 | 0.77 | 75 | empty |
| 2 | 68 | 0.70 | 0.96 | 21 | empty |
| 3 | 701 | 0.69 | 0.77 | 66 | empty |
| 4 | 56 | 0.66 | 0.96 | 21 | empty |
| 5 | 360 | 0.62 | 0.78 | 48 | empty |
Interfaces
4 interfaces between chains.
- C–D · 828 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 491 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5M94 · Crystal structure of Staphylococcus capitis divalent metal ion transporter (DMT) in… · 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 5M94 · PDBe 5M94 · UniProt A0A0S4MEX1
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