9OZO
Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 2.2 A resolution from a 2-day old crystal
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B (A, B) | Dermonecrotic toxin StSicTox-betaIB1i | polymer | 301 | 34262.3 | 2 | UniProt (A0A0D4WV12) | Sicarius terrosus | Phospholipase D,PLD,Sphingomyelin phosphodiesterase D,SMD,SMase D,Sphingomyelinase D |
| 2 | C, D, J, K (A, B) | 2-aminoethyl (2S,3R,4E)-2-dodecanamido-3-hydroxyheptadec-4-en-1-yl hydrogen (S)-phosphate | non-polymer | 590.8 | 4 | Chemie (A1A43) | |||
| 3 | E, L (A, B) | N-{(2S,4R,5S)-2-hydroxy-2-oxo-4-[(1E,7Z)-tetradeca-1,7-dien-1-yl]-1,3,2lambda~5~-dioxaphosphinan-5-yl}dodecanamide | non-polymer | 529.7 | 2 | Chemie (A1A44) | |||
| 4 | F, M (A, B) | SODIUM ION | non-polymer | 23.0 | 2 | Chemie (NA) PubChem (923) | |||
| 5 | G, N (A, B) | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) PubChem (888) | |||
| 6 | H, I (A) | (4S)-2-METHYL-2,4-PENTANEDIOL | non-polymer | 118.2 | 2 | Chemie (MPD) PubChem (5288834) | |||
| 7 | O, P (A, B) | water | water | 18.0 | 851 | Chemie (HOH) |
Sequence modifications
A, B: 0 - 278 (UniProt: A0A0D4WV12)
| PDB | External Database | Details |
|---|---|---|
| Met -22 | - | expression tag |
| Lys -21 | - | expression tag |
| His -20 | - | expression tag |
| His -19 | - | expression tag |
| His -18 | - | expression tag |
| His -17 | - | expression tag |
| His -16 | - | expression tag |
| His -15 | - | expression tag |
| His -14 | - | expression tag |
| His -13 | - | expression tag |
| Gly -12 | - | expression tag |
| Gly -11 | - | expression tag |
| Leu -10 | - | expression tag |
| Val -9 | - | expression tag |
| Pro -8 | - | expression tag |
| Arg -7 | - | expression tag |
| Gly -6 | - | expression tag |
| Ser -5 | - | expression tag |
| His -4 | - | expression tag |
| Gly -3 | - | expression tag |
| Gly -2 | - | expression tag |
| Ser -1 | - | expression tag |
| Asn 47 | His 48 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total formula weight | 68524.7 | |
| Non-Polymers* | Number of molecules | 12 |
| Total formula weight | 3753.7 | |
| All* | Total formula weight | 72278.3 |
