MolNFT v1 · #184336 · protein
Cryo-EM structure of N. gonorhoeae lptde in complex with promacrobodies (mbps have not been built de novo)
7OMM · Lps-assembly protein lptd: “Cryo-EM structure of N. gonorhoeae lptde in complex with promacrobodies (mbps have not been built de novo)”. Electron microscopy, 16 pockets (best druggability 0.83). MolNFT v1 #184336 on GenesisL1: 3D…
- PDB
- 7OMM
- Type
- protein
- Length
- 1,794 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lps-assembly protein lptd; Lps-assembly lipoprotein lpte; Promacrobody…
- UniProt
- Q5F651, A0A5K1Q6A7, A0A0F8L1I7
- Pockets
- 16 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lps-assembly protein lptd | protein | 698 | 1% helix, 36% strand | Q5F651 |
| B | Lps-assembly lipoprotein lpte | protein | 128 | 31% helix, 30% strand | A0A5K1Q6A7 |
| C | Promacrobody 21,MALTODEXTRIN-binding protein | protein | 479 | 35% helix, 27% strand | A0A0F8L1I7 |
| D | Promacrobody 51,MALTODEXTRIN-binding protein | protein | 489 | 35% helix, 15% strand | A0A0F8L1I7 |
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.83 | 0.87 | 80 | empty |
| 2 | 878 | 0.83 | 0.85 | 95 | empty |
| 3 | 266 | 0.76 | 0.89 | 39 | empty |
| 4 | 222 | 0.75 | 0.90 | 45 | empty |
| 5 | 397 | 0.70 | 0.82 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2219 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 684 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 552 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 62 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 46 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7OMM · Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies (MBPs have not… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5F651 · AlphaFold monomer V2.0 prediction for lps-assembly protein lptd (Q5F651) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q5F651
- Every structure of UniProt A0A5K1Q6A7
- Every structure of UniProt A0A0F8L1I7
- Elsewhere: RCSB PDB 7OMM · PDBe 7OMM · UniProt Q5F651 · UniProt A0A5K1Q6A7 · UniProt A0A0F8L1I7
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