Research workbench
Bamabcde in MSP1D1 nanodisc ensemble 1-2
Analyse Bamabcde in MSP1D1 nanodisc ensemble 1-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SO7
- Type
- protein
- Length
- 1,518 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; Outer membrane protein assembly factor bamb…
- UniProt
- B7MBF8, A0A2S5ZNM3, A0A4T5IPK3, P0AC04, P0A938
- Pockets
- 10 · best druggability 0.71
Structure
electron microscopy · 5 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 783 | 16% helix, 39% strand | B7MBF8 |
| B | Outer membrane protein assembly factor bamb | protein | 371 | 0% helix, 35% strand | A0A2S5ZNM3 |
| C | Outer membrane protein assembly factor bamc | protein | 59 | 7% helix, 0% strand | A0A4T5IPK3 |
| D | Outer membrane protein assembly factor bamd | protein | 218 | 74% helix, 0% strand | P0AC04 |
| E | Outer membrane protein assembly factor bame | protein | 87 | 15% helix, 30% strand | P0A938 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.71 | 0.82 | 39 | empty |
| 2 | 312 | 0.55 | 0.76 | 40 | empty |
| 3 | 281 | 0.55 | 0.76 | 36 | empty |
| 4 | 221 | 0.53 | 0.77 | 32 | empty |
| 5 | 166 | 0.50 | 0.78 | 29 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2360 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 1660 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 1464 Ų buried · 45 hydrogen bonds · protein-protein
- D–E · 789 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 683 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6SO7 · BamABCDE in MSP1D1 nanodisc ensemble 1-2 · the same entry in another collection · chain E against E, TM-score 1.00
- P0AC04 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamd (P0AC04) · a predicted model of the same protein · chain D against A, TM-score 0.92
- P0A938 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bame (P0A938) · a predicted model of the same protein · chain E against A, TM-score 0.77
- B7MBF8 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bama (B7MBF8) · a predicted model of the same protein · chain A against A, TM-score 0.58
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 B7MBF8
- Every structure of UniProt A0A2S5ZNM3
- Every structure of UniProt A0A4T5IPK3
- Every structure of UniProt P0AC04
- Every structure of UniProt P0A938
- Elsewhere: RCSB PDB 6SO7 · PDBe 6SO7 · UniProt B7MBF8 · UniProt A0A2S5ZNM3 · UniProt A0A4T5IPK3 · UniProt P0AC04 · UniProt P0A938
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