Research workbench
Structure of homo-dimeric staphylococcus capitis divalent metal ion transporter (dmt) by nabfab-fiducial assisted cryo-EM
Analyse Structure of homo-dimeric 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
- 7PHQ
- Type
- protein
- Length
- 2,136 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nabfab hc; Nabfab lc; Divalent metal cation transporter mnth; Dmt-NB16_4; Anti-Fab…
- UniProt
- A0A4U9TNH6
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 5 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | Nabfab hc | protein | 221 | 9% helix, 44% strand | — |
| L, C | Nabfab lc | protein | 208 | 4% helix, 43% strand | — |
| B, D | Divalent metal cation transporter mnth | protein | 398 | 78% helix, 0% strand | A0A4U9TNH6 |
| N, E | Dmt-NB16_4 | protein | 121 | 0% helix, 32% strand | — |
| K, F | Anti-Fab nanobody | protein | 120 | 8% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.74 | 0.78 | 78 | empty |
| 2 | 775 | 0.73 | 0.78 | 78 | empty |
| 3 | 299 | 0.61 | 0.79 | 42 | empty |
| 4 | 430 | 0.60 | 0.75 | 69 | empty |
| 5 | 378 | 0.58 | 0.75 | 54 | empty |
Interfaces
11 interfaces between chains.
- H–L · 1905 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1904 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 813 Ų buried · 11 hydrogen bonds · protein-protein
- B–N · 813 Ų buried · 11 hydrogen bonds · protein-protein
- H–N · 765 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7PHQ · Structure of homo-dimeric Staphylococcus capitis divalent metal ion transporter (DMT) by… · the same entry in another collection · chain L against L, 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 A0A4U9TNH6
- Elsewhere: RCSB PDB 7PHQ · PDBe 7PHQ · UniProt A0A4U9TNH6
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