Research workbench
The structure of the bamacde subcomplex from E. COLI
Analyse The structure of the bamacde subcomplex from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EKQ
- Type
- protein
- Length
- 1,251 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; Outer membrane protein assembly factor bamd…
- UniProt
- P0A940, P0AC02, P0A903, P0A937
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 763 | 14% helix, 36% strand | P0A940 |
| D | Outer membrane protein assembly factor bamd | protein | 219 | 68% helix, 0% strand | P0AC02 |
| C | Outer membrane protein assembly factor bamc | protein | 179 | 21% helix, 13% strand | P0A903 |
| E | Outer membrane protein assembly factor bame | protein | 90 | 3% helix, 34% strand | P0A937 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.79 | 0.86 | 53 | empty |
| 2 | 284 | 0.70 | 0.84 | 42 | empty |
| 3 | 52 | 0.67 | 0.96 | 25 | empty |
| 4 | 263 | 0.65 | 0.82 | 35 | empty |
| 5 | 243 | 0.61 | 0.80 | 35 | empty |
Interfaces
5 interfaces between chains.
- D–C · 2525 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1151 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 838 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 794 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 135 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5EKQ · The structure of the BamACDE subcomplex from E. coli · the same entry in another collection · chain E against E, TM-score 1.00
- P0AC02 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamd (P0AC02) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P0A903 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamc (P0A903) · a predicted model of the same protein · chain C against A, TM-score 0.93
- P0A937 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bame (P0A937) · a predicted model of the same protein · chain E against A, TM-score 0.88
- P0A940 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bama (P0A940) · a predicted model of the same protein · chain A against A, TM-score 0.60
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 P0A940
- Every structure of UniProt P0AC02
- Every structure of UniProt P0A903
- Every structure of UniProt P0A937
- Elsewhere: RCSB PDB 5EKQ · PDBe 5EKQ · UniProt P0A940 · UniProt P0AC02 · UniProt P0A903 · UniProt P0A937
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