MolNFT v1 · #143520 · protein
Capsid protein and C-terminal part of cpmb protein in the staphylococcus aureus pathogenicity island 1 80ALPHA-derived procapsid
6B23 · Major head protein: “Capsid protein and C-terminal part of cpmb protein in the staphylococcus aureus pathogenicity island 1…”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #143520 on GenesisL1: 3D structure…
- PDB
- 6B23
- Type
- protein
- Length
- 1,232 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major head protein; Capsid morphogenesis B protein
- UniProt
- A4ZFB3, O54465
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 33% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Major head protein | protein | 284 | 26% helix, 15% strand | A4ZFB3 |
| a, b | Capsid morphogenesis B protein | protein | 15 | 53% helix, 0% strand | O54465 |
| c, d | Capsid morphogenesis B protein | protein | 33 | 85% helix, 0% strand | O54465 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.85 | 0.86 | 110 | empty |
| 2 | 698 | 0.73 | 0.79 | 75 | empty |
| 3 | 216 | 0.69 | 0.86 | 37 | empty |
| 4 | 208 | 0.67 | 0.85 | 30 | empty |
| 5 | 359 | 0.65 | 0.80 | 43 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1598 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1481 Ų buried · 10 hydrogen bonds · protein-protein
- C–c · 701 Ų buried · 7 hydrogen bonds · protein-protein
- b–B · 647 Ų buried · 5 hydrogen bonds · protein-protein
- D–d · 629 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6B23 · Capsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus… · the same entry in another collection · chain A against A, 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 A4ZFB3
- Every structure of UniProt O54465
- Elsewhere: RCSB PDB 6B23 · PDBe 6B23 · UniProt A4ZFB3 · UniProt O54465
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