Research workbench
Crystal structure of staphylococcus capitis divalent metal ion transporter (dmt) in complex with nanobody
Analyse Crystal structure of staphylococcus capitis divalent metal ion transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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