SMTL ID : 4gv5.2 (2 other biounits)

X-ray structure of crotamine, a cell-penetrating peptide from the Brazilian snake Crotalus durissus terrificus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

8 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 5 residues within 4Å: Chain A: K.16, I.17 Chain C: Y.1, R.31, W.34 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.1 Water bridges: C:R.31 SCN.2: 7 residues within 4Å: Chain A: P.13, K.14, E.15, R.33 Chain B: P.21 Chain C: F.12, P.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.15 SCN.7: 4 residues within 4Å: Chain A: I.17 Chain B: I.17, G.42 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.42 SCN.9: 2 residues within 4Å: Chain C: W.32, R.33 No protein-ligand interaction detected (PLIP) SCN.12: 5 residues within 4Å: Chain D: K.16, I.17 Chain F: Y.1, R.31, W.34 1 PLIP interactions: 1 interactions with chain F Water bridges: F:R.31 SCN.13: 7 residues within 4Å: Chain D: P.13, K.14, E.15, R.33 Chain E: P.21 Chain F: F.12, P.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.15 SCN.18: 4 residues within 4Å: Chain D: I.17 Chain E: I.17, G.42 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.42 SCN.20: 2 residues within 4Å: Chain F: W.32, R.33 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.14, W.32, R.33 Chain B: P.21, S.22 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.21, A:K.14, A:R.33 GOL.4: 2 residues within 4Å: Chain A: W.32, R.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.33, A:R.33 GOL.10: 8 residues within 4Å: Chain B: I.17, L.19, G.42 Chain C: R.31, W.32, R.33, W.34 Ligands: SCN.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.31, C:R.31, C:W.32, C:R.33 GOL.11: 8 residues within 4Å: Chain B: L.19, P.20, P.21 Chain C: P.13, K.14, E.15, K.16 Chain F: P.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.15 GOL.14: 5 residues within 4Å: Chain D: K.14, W.32, R.33 Chain E: P.21, S.22 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:K.14, D:R.33, E:P.21 GOL.15: 2 residues within 4Å: Chain D: W.32, R.33 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.33, D:R.33 GOL.21: 8 residues within 4Å: Chain E: I.17, L.19, G.42 Chain F: R.31, W.32, R.33, W.34 Ligands: SCN.18 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.31, F:R.31, F:W.32, F:R.33 GOL.22: 8 residues within 4Å: Chain C: P.21 Chain E: L.19, P.20, P.21 Chain F: P.13, K.14, E.15, K.16 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.15

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain B: W.32, R.33 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.33 SO4.6: 3 residues within 4Å: Chain B: Y.1, H.10, C.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.11 Salt bridges: B:H.10 SO4.8: 5 residues within 4Å: Chain A: F.12, P.13, K.16 Chain C: H.10, C.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:K.16 Salt bridges: A:K.16, C:H.10 Hydrogen bonds: C:C.11 SO4.16: 2 residues within 4Å: Chain E: W.32, R.33 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.33 SO4.17: 3 residues within 4Å: Chain E: Y.1, H.10, C.11 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:C.11 Water bridges: E:Y.1, E:Y.1 Salt bridges: E:H.10 SO4.19: 5 residues within 4Å: Chain D: F.12, P.13, K.16 Chain F: H.10, C.11 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F Water bridges: D:K.16 Salt bridges: D:K.16, F:H.10 Hydrogen bonds: F:C.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coronado, M.A. et al., Structure of the polypeptide crotamine from the Brazilian rattlesnake Crotalus durissus terrificus. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-09-04

Peptides

Crotamine Ile-19: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Crotamine Ile-19

Related Entries With Identical Sequence