SMTL ID : 8bbu.1

Crystal structure of medical leech destabilase (high salt)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-dimer

Ligands

3 x NA: SODIUM ION(Non-functional Binders)

NA.1: 1 residues within 4Å: Chain A: Q.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.36 NA.2: 2 residues within 4Å: Chain A: G.15, S.18 No protein-ligand interaction detected (PLIP) NA.10: 1 residues within 4Å: Chain B: D.26 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.93 Water bridges: B:E.14, B:E.14, B:N.93

7 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 7 residues within 4Å: Chain A: G.49, G.50, S.54, C.55, N.58, C.61 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.50 Water bridges: A:N.58, A:N.58, A:N.58 MLI.4: 2 residues within 4Å: Chain A: H.119 Ligands: MLI.5 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.119, A:H.119 MLI.5: 3 residues within 4Å: Chain A: T.118, H.119 Ligands: MLI.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.119 Water bridges: A:H.119, A:H.120 Salt bridges: A:H.119 MLI.6: 3 residues within 4Å: Chain A: C.85, L.115, R.116 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.115 Hydrogen bonds: A:C.85 MLI.9: 8 residues within 4Å: Chain A: T.75, F.76, G.80 Chain B: C.85, W.108, Q.112, L.115, R.116 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.108 Hydrogen bonds: B:Q.112 Water bridges: B:C.85, B:R.116 Salt bridges: B:R.116 MLI.11: 6 residues within 4Å: Chain B: G.49, G.50, S.54, C.55, N.58, C.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.50 Water bridges: B:S.54 MLI.12: 3 residues within 4Å: Chain B: C.23, E.53, K.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.53 Salt bridges: B:K.57

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: P.40, Y.41, D.44, Y.69, G.95, P.96 Chain B: T.82 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.44, A:Y.69 Water bridges: A:G.94, B:T.82 GOL.8: 5 residues within 4Å: Chain A: I.20, G.21, K.57, N.58 Ligands: MLI.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.58 Water bridges: A:S.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marin, E. et al., Structural insights into thrombolytic activity of destabilase from medicinal leech. Sci Rep (2023)

Release Date

2023-02-08

Peptides

Lysozyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysozyme

Related Entries With Identical Sequence