Research workbench
Lateral-open conformation of the lid-locked bam complex (bama E435C S665C, bambdce) by cryoem
Analyse Lateral-open conformation of the lid-locked bam complex (bama E435C S665C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NBX
- Type
- protein
- Length
- 1,475 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
- P0A940, P77774, P0A903, P0AC02, P0A937
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 761 | 15% helix, 39% strand | P0A940 |
| B | Outer membrane protein assembly factor bamb | protein | 357 | 0% helix, 34% strand | P77774 |
| C | Outer membrane protein assembly factor bamc | protein | 56 | 0% helix, 0% strand | P0A903 |
| D | Outer membrane protein assembly factor bamd | protein | 218 | 68% helix, 0% strand | P0AC02 |
| E | Outer membrane protein assembly factor bame | protein | 83 | 14% helix, 33% strand | P0A937 |
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 | 950 | 0.85 | 0.86 | 128 | empty |
| 2 | 309 | 0.81 | 0.91 | 74 | empty |
| 3 | 411 | 0.79 | 0.87 | 61 | empty |
| 4 | 394 | 0.74 | 0.85 | 58 | empty |
| 5 | 102 | 0.74 | 0.95 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1815 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1304 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1118 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 742 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 672 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7NBX · Lateral-open conformation of the lid-locked BAM complex (BamA E435C S665C, BamBDCE) by… · the same entry in another collection · chain E against E, 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 0.96
- 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 0.93
- 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
- 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 0.59
- 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 0.55
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 P0A903
- Every structure of UniProt P0AC02
- Every structure of UniProt P0A937
- Elsewhere: RCSB PDB 7NBX · PDBe 7NBX · UniProt P0A940 · UniProt P77774 · UniProt P0A903 · UniProt P0AC02 · UniProt P0A937
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