Research workbench
Bamacde complex, outer membrane beta-barrel assembly machinery (bam) complex
Analyse Bamacde complex, outer membrane beta-barrel assembly machinery (bam) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D0Q
- Type
- protein
- Length
- 2,535 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; Outer membrane protein assembly factor bamc…
- UniProt
- P0A940, P0A903, P0AC02, P0A937
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 762 | 15% helix, 40% strand | P0A940 |
| C | Outer membrane protein assembly factor bamc | protein | 316 | 27% helix, 27% strand | P0A903 |
| D, H | Outer membrane protein assembly factor bamd | protein | 218 | 76% helix, 0% strand | P0AC02 |
| E, I | Outer membrane protein assembly factor bame | protein | 87 | 14% helix, 32% strand | P0A937 |
| F | Outer membrane protein assembly factor bama | protein | 761 | 16% helix, 40% strand | P0A940 |
| G | Outer membrane protein assembly factor bamc | protein | 86 | 15% helix, 0% strand | P0A903 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.79 | 0.81 | 96 | empty |
| 2 | 462 | 0.76 | 0.85 | 45 | empty |
| 3 | 1035 | 0.76 | 0.78 | 119 | empty |
| 4 | 764 | 0.74 | 0.79 | 79 | empty |
| 5 | 67 | 0.71 | 0.96 | 22 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2715 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2322 Ų buried · 25 hydrogen bonds · protein-protein
- F–H · 1486 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1316 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 836 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 modified (engineered).
Compared structures
- P0AC02 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamd (P0AC02) · a predicted model of the same protein · chain H against A, TM-score 0.96
- P0A937 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bame (P0A937) · a predicted model of the same protein · chain I against A, TM-score 0.89
- P0A903 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamc (P0A903) · a predicted model of the same protein · chain G against A, TM-score 0.87
- P0A940 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bama (P0A940) · a predicted model of the same protein · chain F against A, TM-score 0.63
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 P0A903
- Every structure of UniProt P0AC02
- Every structure of UniProt P0A937
- Elsewhere: RCSB PDB 5D0Q · PDBe 5D0Q · UniProt P0A940 · UniProt P0A903 · UniProt P0AC02 · UniProt P0A937
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