Research workbench
Anthrax octamer prechannel bound to full-length edema factor
Analyse Anthrax octamer prechannel bound to full-length edema factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VRA
- Type
- protein
- Length
- 7,208 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protective antigen; Calmodulin-sensitive adenylate cyclase
- EC
- 4.6.1.1
- UniProt
- P13423, P40136
- Ligands
- CA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 27% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Protective antigen | protein | 541 | 15% helix, 30% strand | P13423 |
| B, D, F, H | Protective antigen | protein | 541 | 16% helix, 29% strand | P13423 |
| I, J, K, L | Calmodulin-sensitive adenylate cyclase (EC 4.6.1.1) | protein | 720 | 45% helix, 5% strand | P40136 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 947 | 0.81 | 0.83 | 106 | empty |
| 2 | 1085 | 0.80 | 0.81 | 110 | empty |
| 3 | 1132 | 0.79 | 0.81 | 111 | empty |
| 4 | 1126 | 0.79 | 0.81 | 109 | empty |
| 5 | 1128 | 0.79 | 0.81 | 106 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1556 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1554 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1550 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1549 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1497 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6VRA · Anthrax octamer prechannel bound to full-length edema factor · the same entry in another collection · chain L against L, TM-score 1.00
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 P13423
- Every structure of UniProt P40136
- Elsewhere: RCSB PDB 6VRA · PDBe 6VRA · UniProt P13423 · UniProt P40136
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