MolNFT v1 · #188470 · protein
Bamabcde bound to substrate espp
7TTC · Outer membrane protein assembly factor bamb: “Bamabcde bound to substrate espp”. Electron microscopy, 1 ligand (K33), 17 pockets (best druggability 0.78). MolNFT v1 #188470 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7TTC
- Type
- protein
- Length
- 1,300 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bamb; Outer membrane protein assembly factor bama…
- UniProt
- P77774, C3TPJ2, A0A3L5AP29, A0A1X3I1M6, W8SZY2, Q7BSW5
- Ligands
- K33
- Pockets
- 17 · best druggability 0.78
Structure
electron microscopy · 6 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Outer membrane protein assembly factor bamb | protein | 327 | 1% helix, 45% strand | P77774 |
| A | Outer membrane protein assembly factor bama | protein | 600 | 14% helix, 46% strand | C3TPJ2 |
| E | Outer membrane protein assembly factor bame | protein | 86 | 14% helix, 40% strand | A0A3L5AP29 |
| D | Outer membrane protein assembly factor bamd | protein | 211 | 77% helix, 0% strand | A0A1X3I1M6 |
| C | Outer membrane protein assembly factor bamc | protein | 48 | 15% helix, 0% strand | W8SZY2 |
| P | Serine protease espp | protein | 28 | 0% helix, 54% strand | Q7BSW5 |
Ligands and binding sites
- K33 · 2,3-dideoxy-6-O-[2-deoxy-4-O-phosphono-2-(tetradecanoylamino)-alpha-L-gulopyranosyl]-1-O-phosphono-beta-D-threo-hexopyranose · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.78 | 0.80 | 87 | empty |
| 2 | 816 | 0.75 | 0.80 | 76 | empty |
| 3 | 292 | 0.70 | 0.84 | 33 | empty |
| 4 | 369 | 0.63 | 0.78 | 53 | empty |
| 5 | 147 | 0.61 | 0.84 | 30 | empty |
Interfaces
8 interfaces between chains.
- D–C · 1792 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 954 Ų buried · 12 hydrogen bonds · protein-protein
- E–D · 814 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 813 Ų buried · 8 hydrogen bonds · protein-protein
- A–P · 714 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7TTC · BamABCDE bound to substrate EspP · the same entry in another collection · chain P against P, TM-score 1.00
- P77774 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamb (P77774) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q7BSW5 · AlphaFold monomer V2.0 prediction for serine protease espp (Q7BSW5) · a predicted model of the same protein · chain P against A, TM-score 0.56
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 P77774
- Every structure of UniProt C3TPJ2
- Every structure of UniProt A0A3L5AP29
- Every structure of UniProt A0A1X3I1M6
- Every structure of UniProt W8SZY2
- Every structure of UniProt Q7BSW5
- Elsewhere: RCSB PDB 7TTC · PDBe 7TTC · UniProt P77774 · UniProt C3TPJ2 · UniProt A0A3L5AP29 · UniProt A0A1X3I1M6 · UniProt W8SZY2 · UniProt Q7BSW5
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