SMTL ID : 5f2q.1

C-type lectin from Bothrops jararacussu

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-10-mer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: Q.96, D.98, E.104, N.119, D.120 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.98, A:E.104, A:D.120, A:D.120, H2O.1 CA.3: 5 residues within 4Å: Chain B: Q.96, D.98, E.104, N.119, D.120 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.98, B:E.104, B:D.120, B:D.120, H2O.1 CA.5: 5 residues within 4Å: Chain C: Q.96, D.98, E.104, N.119, D.120 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.98, C:E.104, C:D.120, C:D.120 CA.7: 5 residues within 4Å: Chain D: Q.96, D.98, E.104, N.119, D.120 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.98, D:E.104, D:D.120, D:D.120, H2O.1 CA.9: 5 residues within 4Å: Chain E: Q.96, D.98, E.104, N.119, D.120 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.98, E:E.104, E:D.120, E:D.120, H2O.1 CA.11: 5 residues within 4Å: Chain F: Q.96, D.98, E.104, N.119, D.120 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.98, F:E.104, F:D.120, F:D.120, H2O.1 CA.13: 5 residues within 4Å: Chain G: Q.96, D.98, E.104, N.119, D.120 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.98, G:E.104, G:D.120, G:D.120, H2O.1 CA.15: 5 residues within 4Å: Chain H: Q.96, D.98, E.104, N.119, D.120 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.98, H:D.120, H:D.120, H2O.1 CA.17: 5 residues within 4Å: Chain I: Q.96, D.98, E.104, N.119, D.120 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.98, I:E.104, I:D.120, I:D.120, H2O.2 CA.19: 5 residues within 4Å: Chain J: Q.96, D.98, E.104, N.119, D.120 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.98, J:E.104, J:D.120, J:D.120, H2O.2

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

NA.2: 5 residues within 4Å: Chain A: L.13, Y.15, S.42, H.44, Q.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.15, A:Y.15, A:S.42, A:Q.132 NA.4: 5 residues within 4Å: Chain B: L.13, Y.15, S.42, H.44, Q.132 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.15, B:S.42, B:S.42, B:H.44, B:Q.132 NA.6: 5 residues within 4Å: Chain C: L.13, Y.15, S.42, H.44, Q.132 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.15, C:S.42, C:S.42 NA.8: 5 residues within 4Å: Chain D: L.13, Y.15, S.42, H.44, Q.132 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.15, D:Q.132 NA.10: 5 residues within 4Å: Chain E: L.13, Y.15, S.42, H.44, Q.132 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.15, E:S.42, E:S.42, E:Q.132 NA.12: 5 residues within 4Å: Chain F: L.13, Y.15, S.42, H.44, Q.132 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.15, F:S.42 NA.14: 6 residues within 4Å: Chain G: L.13, Y.15, S.42, I.43, H.44, Q.132 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.15 Water bridges: G:Q.132 NA.16: 5 residues within 4Å: Chain H: L.13, Y.15, S.42, H.44, Q.132 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:Y.15, H:S.42, H:H.44 NA.18: 5 residues within 4Å: Chain I: L.13, Y.15, S.42, H.44, Q.132 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:Y.15, I:S.42, I:H.44 NA.20: 6 residues within 4Å: Chain J: L.13, Y.15, S.42, H.44, D.83, Q.132 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:Y.15, J:S.42, J:Q.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Padua, R.A.P. et al., C-type lectin from Bothrops jararacussu. To Be Published

Release Date

2016-12-07

Peptides

C-type lectin BJcuL: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

C-type lectin BJcuL