MolNFT v1 · #148210 · protein
The crystal structure of secreted antigen BPSL2520
6F03: “The crystal structure of secreted antigen BPSL2520”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.77). MolNFT v1 #148210 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F03
- Type
- protein
- Length
- 641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BPSL2520
- UniProt
- Q63S01
- Ligands
- CA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | BPSL2520 | protein | 159 | 88% helix, 0% strand | Q63S01 |
| B | BPSL2520 | protein | 163 | 87% helix, 0% strand | Q63S01 |
| D | BPSL2520 | protein | 160 | 87% helix, 0% strand | Q63S01 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- ACT · Acetate ion · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.77 | 0.85 | 53 | GOL |
| 2 | 586 | 0.66 | 0.76 | 40 | ACT |
| 3 | 534 | 0.65 | 0.76 | 37 | empty |
| 4 | 181 | 0.56 | 0.80 | 24 | empty |
| 5 | 54 | 0.50 | 0.86 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3062 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 3023 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 235 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 210 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 6F03 · The crystal structure of secreted antigen BPSL2520 · 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 Q63S01
- Elsewhere: RCSB PDB 6F03 · PDBe 6F03 · UniProt Q63S01
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