SMTL ID : 2jdz.1

Crystal structure of recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

20 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: E.10, D.12, D.21, H.26 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.10, A:D.12, A:D.21, A:H.26, H2O.3, H2O.3 MN.3: 3 residues within 4Å: Chain A: N.126, H.182 Chain B: S.136 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.182, H2O.3, H2O.3, H2O.3 MN.5: 3 residues within 4Å: Chain A: S.127 Chain B: H.129, S.131 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:S.127, B:H.129, H2O.3, H2O.3, H2O.3 MN.6: 1 residues within 4Å: Chain A: D.207 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.207, A:D.207, H2O.3 MN.7: 2 residues within 4Å: Chain A: H.53, D.194 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.53, A:D.194, A:D.194, H2O.3, H2O.4 MN.9: 4 residues within 4Å: Chain B: E.10, D.12, D.21, H.26 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.10, B:D.12, B:D.21, B:H.26, H2O.6, H2O.6 MN.11: 3 residues within 4Å: Chain A: S.136 Chain B: N.126, H.182 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.182, H2O.6, H2O.6, H2O.6 MN.13: 3 residues within 4Å: Chain A: H.129, S.131 Chain B: S.127 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:S.127, A:H.129, H2O.6, H2O.6, H2O.6 MN.14: 1 residues within 4Å: Chain B: D.207 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.207, B:D.207, H2O.6 MN.15: 2 residues within 4Å: Chain B: H.53, D.194 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.53, B:D.194, B:D.194, H2O.7, H2O.7 MN.17: 4 residues within 4Å: Chain C: E.10, D.12, D.21, H.26 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.10, C:D.12, C:D.21, C:H.26, H2O.9, H2O.9 MN.19: 3 residues within 4Å: Chain C: N.126, H.182 Chain D: S.136 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.182, H2O.9, H2O.9, H2O.9 MN.21: 3 residues within 4Å: Chain C: S.127 Chain D: H.129, S.131 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:H.129, C:S.127, H2O.9, H2O.9, H2O.10 MN.22: 1 residues within 4Å: Chain C: D.207 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.207, C:D.207, H2O.10 MN.23: 2 residues within 4Å: Chain C: H.53, D.194 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.53, C:D.194, C:D.194, H2O.10, H2O.10 MN.25: 4 residues within 4Å: Chain D: E.10, D.12, D.21, H.26 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.10, D:D.12, D:D.21, D:H.26, H2O.12, H2O.12 MN.27: 3 residues within 4Å: Chain C: S.136 Chain D: N.126, H.182 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.182, H2O.12, H2O.12, H2O.12 MN.29: 3 residues within 4Å: Chain C: H.129, S.131 Chain D: S.127 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:H.129, D:S.127, H2O.13, H2O.13, H2O.13 MN.30: 1 residues within 4Å: Chain D: D.207 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.207, D:D.207, H2O.13 MN.31: 2 residues within 4Å: Chain D: H.53, D.194 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.53, D:D.194, D:D.194, H2O.13, H2O.13

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.12, Y.14, N.16, D.21 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.12, A:D.12, A:Y.14, A:D.21, H2O.3 CA.10: 4 residues within 4Å: Chain B: D.12, Y.14, N.16, D.21 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.12, B:D.12, B:Y.14, B:D.21, H2O.6 CA.18: 4 residues within 4Å: Chain C: D.12, Y.14, N.16, D.21 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.12, C:D.12, C:Y.14, C:D.21, H2O.9 CA.26: 4 residues within 4Å: Chain D: D.12, Y.14, N.16, D.21 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.12, D:D.12, D:Y.14, D:D.21, H2O.12

4 x CD: CADMIUM ION(Non-covalent)

CD.4: 2 residues within 4Å: Chain A: E.89, E.185 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.89, A:E.185 CD.12: 2 residues within 4Å: Chain B: E.89, E.185 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.89, B:E.185 CD.20: 2 residues within 4Å: Chain C: E.89, E.185 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.89, C:E.185 CD.28: 2 residues within 4Å: Chain D: E.89, E.185 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.89, D:E.185

4 x XMM: 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside(Non-covalent)

XMM.8: 9 residues within 4Å: Chain A: Y.14, N.16, G.100, L.101, Y.102, A.209, D.210, G.229, R.230 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.101 Hydrogen bonds: A:Y.14, A:N.16, A:G.100, A:L.101, A:Y.102, A:Y.102, A:R.230 Water bridges: A:R.230 XMM.16: 9 residues within 4Å: Chain B: Y.14, N.16, G.100, L.101, Y.102, A.209, D.210, G.229, R.230 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.101 Hydrogen bonds: B:Y.14, B:Y.14, B:N.16, B:G.100, B:L.101, B:Y.102, B:Y.102, B:R.230 Water bridges: B:R.230 XMM.24: 9 residues within 4Å: Chain C: Y.14, N.16, G.100, L.101, Y.102, A.209, D.210, G.229, R.230 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.101 Hydrogen bonds: C:Y.14, C:N.16, C:G.100, C:L.101, C:Y.102, C:Y.102, C:R.230 Water bridges: C:R.230 XMM.32: 9 residues within 4Å: Chain D: Y.14, N.16, G.100, L.101, Y.102, A.209, D.210, G.229, R.230 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.101 Hydrogen bonds: D:Y.14, D:Y.14, D:N.16, D:G.100, D:L.101, D:Y.102, D:Y.102, D:R.230 Water bridges: D:R.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagano, C.S. et al., Insights Into the Structural Basis of the Ph-Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis of Recombinant Diocleinae Lectins. Biochem.J. (2008)

Release Date

2007-10-30

Peptides

LECTIN ALPHA CHAIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

LECTIN ALPHA CHAIN