Research workbench
Structure of the bam complex
Analyse Structure of the bam complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LYS
- Type
- protein
- Length
- 1,582 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; Outer membrane protein assembly factor bamb…
- UniProt
- P0A940, P77774, P0AC02, P0A937, P0A903
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 786 | 16% helix, 42% strand | P0A940 |
| B | Outer membrane protein assembly factor bamb | protein | 351 | 0% helix, 44% strand | P77774 |
| D | Outer membrane protein assembly factor bamd | protein | 208 | 75% helix, 0% strand | P0AC02 |
| E | Outer membrane protein assembly factor bame | protein | 83 | 10% helix, 37% strand | P0A937 |
| C | Outer membrane protein assembly factor bamc | protein | 154 | 16% helix, 25% strand | P0A903 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.77 | 0.84 | 71 | empty |
| 2 | 635 | 0.70 | 0.78 | 55 | empty |
| 3 | 302 | 0.59 | 0.78 | 34 | empty |
| 4 | 258 | 0.56 | 0.77 | 33 | empty |
| 5 | 247 | 0.55 | 0.78 | 35 | empty |
Interfaces
7 interfaces between chains.
- D–C · 2249 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1650 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1208 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 809 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 724 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6LYS · Structure of the BAM complex · the same entry in another collection · chain C against C, 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 0.98
- 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 0.97
- 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 0.95
- 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 0.93
- 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 0.62
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 P77774
- Every structure of UniProt P0AC02
- Every structure of UniProt P0A937
- Every structure of UniProt P0A903
- Elsewhere: RCSB PDB 6LYS · PDBe 6LYS · UniProt P0A940 · UniProt P77774 · UniProt P0AC02 · UniProt P0A937 · UniProt P0A903
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