SMTL ID : 6tmy.1 (1 other biounit)

Crystal structure of isoform CBd of the basic phospholipase A2 subunit of crotoxin from Crotalus durissus terrificus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: Y.27, G.29, W.30, G.31, D.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.31 Water bridges: A:G.31 NA.7: 3 residues within 4Å: Chain A: F.23, G.25, Y.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.23 NA.8: 6 residues within 4Å: Chain B: Y.27, G.29, W.30, G.31, D.48 Ligands: PG4.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.27 NA.11: 4 residues within 4Å: Chain B: F.23, Y.24, G.25, Y.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.23, B:Y.110 NA.13: 4 residues within 4Å: Chain C: Y.27, G.29, G.31, D.48 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.48 Water bridges: C:G.31 NA.16: 3 residues within 4Å: Chain C: F.23, G.25, Y.110 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.25 Water bridges: C:D.112 NA.17: 4 residues within 4Å: Chain D: Y.27, G.29, G.31, D.48 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.31 Water bridges: D:D.48 NA.22: 3 residues within 4Å: Chain D: F.23, G.25, Y.110 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.110, D:Y.110

9 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 11 residues within 4Å: Chain A: F.5, N.6, I.9, A.17, I.18, Y.21, A.22, Y.27, C.28, G.29, C.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.6, A:G.29 PG4.3: 3 residues within 4Å: Chain A: K.56, W.80 Ligands: CL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.56 PG4.9: 13 residues within 4Å: Chain B: L.2, F.5, N.6, I.9, A.17, Y.21, A.22, Y.27, C.28, G.29, C.44 Ligands: NA.8, PG4.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.29 Water bridges: B:W.30, B:H.47, B:D.48 PG4.10: 7 residues within 4Å: Chain B: L.2, L.3, N.6, I.18, W.30 Chain C: Y.105 Ligands: PG4.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.6 PG4.12: 2 residues within 4Å: Chain C: F.11, R.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.11, C:R.14 PG4.14: 10 residues within 4Å: Chain C: F.5, N.6, I.9, A.17, I.18, A.22, Y.27, C.28, G.29, C.44 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.18 Hydrogen bonds: C:G.29 Water bridges: C:N.6 PG4.18: 13 residues within 4Å: Chain D: L.2, F.5, N.6, A.17, Y.21, A.22, Y.27, C.28, G.29, W.30, C.44, H.47 Ligands: PG4.19 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.29 Water bridges: D:G.29, D:W.30, D:D.48 PG4.19: 7 residues within 4Å: Chain A: Y.105 Chain C: W.61 Chain D: L.2, L.3, I.18, W.30 Ligands: PG4.18 No protein-ligand interaction detected (PLIP) PG4.20: 5 residues within 4Å: Chain D: S.70, Y.72, I.73, T.74, R.90 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.70 Water bridges: D:R.90, D:R.90

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

CL.4: 5 residues within 4Å: Chain A: R.65, Y.66 Chain B: Y.64, R.65, Y.66 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: H.1 Chain B: H.1 Chain C: I.18, P.19, F.23, F.109 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: T.79, W.80 Ligands: PG4.3 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain A: I.18, P.19, F.23, F.109 Chain C: H.1 Chain D: H.1 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain C: R.65, Y.66 Chain D: R.65, Y.66 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nemecz, D. et al., Crystal Structure of Isoform CBd of the Basic Phospholipase A 2 Subunit of Crotoxin: Description of the Structural Framework of CB for Interaction with Protein Targets. Molecules (2020)

Release Date

2020-12-02

Peptides

Phospholipase A2 crotoxin basic subunit CBc: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
C

Phospholipase A2 crotoxin basic subunit CBc

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