Research workbench
N-terminal part (residues 30-212) of porm with the llama nanobody NB01
Analyse N-terminal part (residues 30-212) of porm with the llama nanobody NB01 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EY0
- Type
- protein
- Length
- 1,095 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T9SS component cytoplasmic membrane protein porm; Llama nanobody NB01
- UniProt
- A0A1R4DSC1
- Pockets
- 15 · best druggability 0.67
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | T9SS component cytoplasmic membrane protein porm | protein | 147 | 69% helix, 0% strand | A0A1R4DSC1 |
| B | T9SS component cytoplasmic membrane protein porm | protein | 148 | 68% helix, 0% strand | A0A1R4DSC1 |
| D | T9SS component cytoplasmic membrane protein porm | protein | 144 | 71% helix, 0% strand | A0A1R4DSC1 |
| E | Llama nanobody NB01 | protein | 125 | 11% helix, 46% strand | — |
| F | Llama nanobody NB01 | protein | 131 | 11% helix, 45% strand | — |
| G | Llama nanobody NB01 | protein | 129 | 11% helix, 45% strand | — |
| H | Llama nanobody NB01 | protein | 124 | 11% helix, 44% strand | — |
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.67 | 0.76 | 50 | empty |
| 2 | 324 | 0.58 | 0.77 | 32 | empty |
| 3 | 413 | 0.57 | 0.74 | 41 | empty |
| 4 | 212 | 0.52 | 0.77 | 28 | empty |
| 5 | 130 | 0.47 | 0.78 | 17 | empty |
Interfaces
11 interfaces between chains.
- C–D · 672 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 661 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 639 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 633 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 573 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6EY0 · N-terminal part (residues 30-212) of PorM with the llama nanobody nb01 · 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 A0A1R4DSC1
- Elsewhere: RCSB PDB 6EY0 · PDBe 6EY0 · UniProt A0A1R4DSC1
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