SMTL ID : 1h9p.1

Crystal Structure of Dioclea guianensis Seed Lectin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

12 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:H.24, H2O.1, H2O.1 CD.2: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:Y.12, A:D.19, H2O.1, H2O.5 CD.3: 2 residues within 4Å: Chain A: E.87, E.183 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.87, A:E.87, A:E.183, A:E.183 CD.7: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:H.24, H2O.6, H2O.6 CD.8: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.6, H2O.10 CD.9: 2 residues within 4Å: Chain B: E.87, E.183 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.87, B:E.87, B:E.183, B:E.183 CD.13: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:H.24, H2O.11, H2O.11 CD.14: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:Y.12, C:D.19, H2O.11, H2O.15 CD.15: 2 residues within 4Å: Chain C: E.87, E.183 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.87, C:E.87, C:E.183, C:E.183 CD.19: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:H.24, H2O.16, H2O.16 CD.20: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:Y.12, D:D.19, H2O.16, H2O.20 CD.21: 2 residues within 4Å: Chain D: E.87, E.183 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.87, D:E.87, D:E.183, D:E.183

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

MN.4: 3 residues within 4Å: Chain A: S.125 Chain B: H.127, S.129 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:S.125, B:H.127, H2O.5, H2O.5, H2O.5 MN.5: 1 residues within 4Å: Chain A: D.205 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.205, A:D.205, H2O.5 MN.6: 2 residues within 4Å: Chain A: H.51, D.192 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.51, A:D.192, H2O.5, H2O.5 MN.10: 3 residues within 4Å: Chain A: H.127, S.129 Chain B: S.125 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.127, B:S.125, H2O.10, H2O.10, H2O.10 MN.11: 1 residues within 4Å: Chain B: D.205 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.205, B:D.205, H2O.10 MN.12: 2 residues within 4Å: Chain B: H.51, D.192 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.51, B:D.192, H2O.10, H2O.10 MN.16: 3 residues within 4Å: Chain C: S.125 Chain D: H.127, S.129 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:S.125, D:H.127, H2O.15, H2O.15, H2O.15 MN.17: 1 residues within 4Å: Chain C: D.205 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.205, C:D.205, H2O.15 MN.18: 2 residues within 4Å: Chain C: H.51, D.192 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.51, C:D.192, H2O.15, H2O.15 MN.22: 3 residues within 4Å: Chain C: H.127, S.129 Chain D: S.125 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:H.127, D:S.125, H2O.20, H2O.20, H2O.20 MN.23: 1 residues within 4Å: Chain D: D.205 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.205, D:D.205, H2O.20 MN.24: 2 residues within 4Å: Chain D: H.51, D.192 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.51, D:D.192, H2O.20, H2O.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wah, D.A. et al., Crystal Structure of Native and Cd/Cd-Substituted Dioclea Guianensis Seed Lectin. A Novel Manganese-Binding Site and Structural Basis of Dimer-Tetramer Association. J.Mol.Biol. (2001)

Release Date

2001-03-23

Peptides

LECTIN ALPHA CHAIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

LECTIN ALPHA CHAIN