MolNFT v1 · #183039 · protein
Lateral-open conformation of the wild-type bam complex (bamabcde) bound to a bactericidal Fab fragment
7ND0 · Outer membrane protein assembly factor bama: “Lateral-open conformation of the wild-type bam complex (bamabcde) bound to a bactericidal Fab fragment”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #183039 on…
- PDB
- 7ND0
- Type
- protein
- Length
- 1,960 residues
- Chains
- 7
- 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 0.82
Structure
electron microscopy · 7 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 787 | 17% helix, 36% strand | P0A940 |
| B | Outer membrane protein assembly factor bamb | protein | 371 | 0% helix, 41% strand | P77774 |
| C | Outer membrane protein assembly factor bamc | protein | 61 | 11% helix, 0% strand | P0A903 |
| D | Outer membrane protein assembly factor bamd | protein | 218 | 75% helix, 0% strand | P0AC02 |
| E | Outer membrane protein assembly factor bame | protein | 87 | 13% helix, 28% strand | P0A937 |
| H | FAB1 heavy chain | protein | 221 | 5% helix, 50% strand | — |
| L | FAB1 light chain | protein | 215 | 3% helix, 48% strand | — |
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 | 690 | 0.82 | 0.86 | 96 | empty |
| 2 | 332 | 0.78 | 0.89 | 55 | empty |
| 3 | 215 | 0.77 | 0.91 | 52 | empty |
| 4 | 142 | 0.76 | 0.93 | 32 | empty |
| 5 | 159 | 0.75 | 0.93 | 31 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1992 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1722 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1302 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1132 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 719 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7ND0 · lateral-open conformation of the wild-type BAM complex (BamABCDE) bound to a bactericidal… · the same entry in another collection · chain L against L, TM-score 1.00
- 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 0.94
- 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 0.93
- 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 0.85
- 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 0.69
- 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 0.56
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 7ND0 · PDBe 7ND0 · UniProt P0A940 · UniProt P77774 · UniProt P0A903 · UniProt P0AC02 · UniProt P0A937
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