Research workbench
Bamabcde in MSP1D1 nanodisc ensemble 1-5
Analyse Bamabcde in MSP1D1 nanodisc ensemble 1-5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SOC
- 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
- 13 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 783 | 17% helix, 36% strand | B7MBF8 |
| B | Outer membrane protein assembly factor bamb | protein | 371 | 0% helix, 39% strand | A0A2S5ZNM3 |
| C | Outer membrane protein assembly factor bamc | protein | 59 | 17% 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, 31% strand | P0A938 |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.78 | 0.81 | 93 | empty |
| 2 | 842 | 0.74 | 0.79 | 74 | empty |
| 3 | 233 | 0.74 | 0.88 | 40 | empty |
| 4 | 72 | 0.70 | 0.96 | 20 | empty |
| 5 | 552 | 0.69 | 0.79 | 64 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2336 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 1419 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1214 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 753 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 608 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6SOC · BamABCDE in MSP1D1 nanodisc ensemble 1-5 · 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 0.95
- 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 0.81
- 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 0.57
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 6SOC · PDBe 6SOC · UniProt B7MBF8 · UniProt A0A2S5ZNM3 · UniProt A0A4T5IPK3 · UniProt P0AC04 · UniProt P0A938
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