SMTL ID : 3dsl.1

The Three-dimensional Structure of Bothropasin, the Main Hemorrhagic Factor from Bothrops jararaca venom.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: F.157, N.181, C.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.157, A:F.157, A:N.181

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.10, D.94, C.198, N.201 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.10, A:D.94, A:D.94, A:C.198 CA.3: 6 residues within 4Å: Chain A: V.213, N.216, L.218, E.220, E.223, D.226 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.213, A:L.218, A:E.220, A:E.223, A:D.226 CA.4: 5 residues within 4Å: Chain A: D.277, P.278, E.280, D.292, V.293 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.277, A:P.278, A:E.280, A:D.292, A:V.293 CA.10: 4 residues within 4Å: Chain B: E.10, D.94, C.198, N.201 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.10, B:D.94, B:D.94, B:C.198, H2O.5 CA.11: 6 residues within 4Å: Chain B: V.213, N.216, L.218, E.220, E.223, D.226 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.213, B:L.218, B:E.223, B:E.223 CA.12: 6 residues within 4Å: Chain B: D.277, P.278, A.279, E.280, D.292, V.293 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.277, B:E.280, B:D.292, B:V.293

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.143, H.147, H.153 Ligands: TRP.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.143, A:H.147, A:H.153, TRP.7 ZN.13: 4 residues within 4Å: Chain B: H.143, H.147, H.153 Ligands: TRP.9 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain B Metal complexes: TRP.9, B:H.143, B:H.147

2 x FLE: FUROYL-LEUCINE(Non-covalent)

FLE.6: 6 residues within 4Å: Chain A: P.107, T.108, I.109, G.110, Y.130 Ligands: TRP.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.107, A:I.109, A:Y.130 Hydrogen bonds: A:P.107, A:T.108, A:I.109, A:G.110 FLE.8: 7 residues within 4Å: Chain B: G.106, P.107, T.108, I.109, G.110, Y.130 Ligands: TRP.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:I.109, B:I.109 Hydrogen bonds: B:P.107, W.9

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.7: 13 residues within 4Å: Chain A: I.109, G.110, H.143, E.144, H.147, H.153, I.166, G.168, P.169, T.170, I.171 Ligands: ZN.5, FLE.6 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:I.109, A:H.143, A:I.171, A:I.171 Salt bridges: A:H.143, A:H.147, A:H.153 pi-Stacking: A:H.143, A:H.143 TRP.9: 11 residues within 4Å: Chain B: H.143, E.144, H.147, H.153, I.166, G.168, P.169, T.170, I.171 Ligands: FLE.8, ZN.13 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:H.143, B:I.171, B:I.171 Salt bridges: B:H.143, B:H.147, B:H.153 pi-Stacking: B:H.143, B:H.143

Links

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Citation

Muniz, J.R. et al., The three-dimensional structure of bothropasin, the main hemorrhagic factor from Bothrops jararaca venom: Insights for a new classification of snake venom metalloprotease subgroups. Toxicon (2008)

Release Date

2008-10-21

Peptides

Zinc metalloproteinase-disintegrin bothropasin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Zinc metalloproteinase-disintegrin bothropasin