Research workbench
Crystal structure of the E. COLI bamcd complex
Analyse Crystal structure of the E. COLI bamcd complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TGO
- Type
- protein
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0169 lipoprotein yfio; Lipoprotein 34
- UniProt
- P0AC02, P0A903
- Ligands
- K, NA, CL, PO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0169 lipoprotein yfio | protein | 217 | 75% helix, 0% strand | P0AC02 |
| B | UPF0169 lipoprotein yfio | protein | 218 | 74% helix, 0% strand | P0AC02 |
| C | Lipoprotein 34 | protein | 182 | 23% helix, 28% strand | P0A903 |
| D | Lipoprotein 34 | protein | 186 | 24% helix, 25% strand | P0A903 |
Ligands and binding sites
- K · Potassium ion · metal · chains A, C
- NA · Sodium ion · metal · chains D
- CL · Chloride ion · ion · chains B
- PO4 · Phosphate ion · ion · chains C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.78 | 0.80 | 85 | GOL |
| 2 | 614 | 0.73 | 0.80 | 67 | GOL |
| 3 | 267 | 0.67 | 0.83 | 34 | empty |
| 4 | 285 | 0.62 | 0.80 | 32 | empty |
| 5 | 267 | 0.56 | 0.77 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2353 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 2344 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 341 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 336 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 151 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3TGO · Crystal structure of the E. coli BamCD complex · the same entry in another collection · chain D against D, TM-score 1.00
- 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 0.97
- P0AC02 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamd (P0AC02) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P0AC02
- Every structure of UniProt P0A903
- Elsewhere: RCSB PDB 3TGO · PDBe 3TGO · UniProt P0AC02 · UniProt P0A903
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