SMTL ID : 2je9.1

CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.12, Y.14, N.16, D.21 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.12, A:D.12, A:D.21, H2O.5, H2O.6 CA.6: 4 residues within 4Å: Chain B: D.12, Y.14, N.16, D.21 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.12, B:Y.14, B:D.21, H2O.10, H2O.11 CA.12: 4 residues within 4Å: Chain C: D.12, Y.14, N.16, D.21 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.12, C:Y.14, C:D.21, H2O.14, H2O.14 CA.16: 4 residues within 4Å: Chain D: D.12, Y.14, N.16, D.21 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.12, D:Y.14, D:D.21, H2O.14, H2O.17

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

MN.2: 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.6, H2O.6 MN.7: 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.11, H2O.11 MN.13: 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.14, H2O.14 MN.17: 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.17, H2O.17

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

XMM.3: 9 residues within 4Å: Chain A: 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 A Hydrophobic interactions: A:L.101 Hydrogen bonds: A:Y.14, A:N.16, A:L.101, A:Y.102, A:Y.102, A:R.230 Water bridges: A:Y.102, A:N.170, A:R.230 XMM.8: 9 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:L.101 Hydrogen bonds: 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.14: 9 residues within 4Å: Chain C: Y.14, N.16, G.100, L.101, Y.102, A.209, D.210, G.229, R.230 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.14, C:Y.14, C:N.16, C:G.100, C:L.101, C:Y.102, C:Y.102, C:R.230 XMM.18: 9 residues within 4Å: Chain D: 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 D 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

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: S.136, Q.137 Chain B: H.182, E.185 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Water bridges: B:E.89, B:K.186, B:K.186, B:K.186, A:S.136 Salt bridges: B:H.182 Hydrogen bonds: A:S.136, A:Q.137 SO4.5: 3 residues within 4Å: Chain A: Y.24, A.40, R.41 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.24, A:R.41 Water bridges: A:R.41, A:T.76 SO4.9: 4 residues within 4Å: Chain A: H.182, E.185 Chain B: S.136, Q.137 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.185, A:E.185, B:Q.137 Salt bridges: A:H.182 SO4.10: 3 residues within 4Å: Chain B: K.103, Q.168, G.169 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.169 Salt bridges: B:K.103 SO4.11: 5 residues within 4Å: Chain B: Y.14, N.16, T.17, D.18, R.230 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.18 Salt bridges: B:R.230 SO4.15: 4 residues within 4Å: Chain C: S.136, Q.137 Chain D: H.182, E.185 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.185, C:Q.137 Salt bridges: D:H.182 Water bridges: C:Q.137 SO4.19: 4 residues within 4Å: Chain C: H.182, E.185 Chain D: S.136, Q.137 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.137 Salt bridges: C:H.182

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
B

C
C

D
D

LECTIN ALPHA CHAIN