SMTL ID : 3s67.1

Crystal structure of V57P mutant of human cystatin C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 3 residues within 4Å: Chain A: R.51, R.53 Ligands: PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.51, A:R.51 PEG.2: 7 residues within 4Å: Chain A: A.103, V.104, P.105, G.108, T.109, M.110 Chain B: R.25 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.25, B:R.25, A:V.104 PEG.3: 3 residues within 4Å: Chain A: V.50, R.51 Ligands: PEG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.51 Water bridges: A:R.51 PEG.10: 3 residues within 4Å: Chain B: R.51, R.53 Ligands: PEG.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.51, B:R.51 PEG.11: 7 residues within 4Å: Chain A: R.25 Chain B: A.103, V.104, P.105, G.108, T.109, M.110 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.25, A:R.25, B:V.104 PEG.12: 3 residues within 4Å: Chain B: V.50, R.51 Ligands: PEG.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.51 Water bridges: B:R.51

4 x IMD: IMIDAZOLE(Non-covalent)(Non-functional Binders)

IMD.4: 3 residues within 4Å: Chain A: Y.102 Chain B: Y.102 Ligands: IMD.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.102 pi-Stacking: B:Y.102 IMD.5: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:W.106 IMD.13: 3 residues within 4Å: Chain A: Y.102 Chain B: Y.102 Ligands: IMD.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B pi-Stacking: A:Y.102 Water bridges: B:Y.102 IMD.14: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:W.106

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 1 residues within 4Å: Chain A: V.49 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.24 ACT.7: 1 residues within 4Å: Chain A: L.112 No protein-ligand interaction detected (PLIP) ACT.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.15: 1 residues within 4Å: Chain B: V.49 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.24 ACT.16: 1 residues within 4Å: Chain B: L.112 No protein-ligand interaction detected (PLIP) ACT.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 1 residues within 4Å: Chain A: K.54 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: K.54 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orlikowska, M. et al., Structural characterization of V57D and V57P mutants of human cystatin C, an amyloidogenic protein. Acta Crystallogr.,Sect.D (2013)

Release Date

2012-05-30

Peptides

Cystatin-C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cystatin-C