SMTL ID : 3a0k.1

Crystal structure of an antiflamatory legume lectin from Cymbosema roseum seeds

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.2, H2O.6 MN.3: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.12, H2O.12 MN.5: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.18, H2O.18 MN.8: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.26, H2O.26

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:D.10, A:Y.12, A:D.19, H2O.1 CA.4: 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:D.10, B:D.19, H2O.8, H2O.12 CA.6: 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.15, H2O.16 CA.9: 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:D.10, D:D.19, H2O.23, H2O.26

2 x ABA: ALPHA-AMINOBUTYRIC ACID(Non-functional Binders)

ABA.7: 9 residues within 4Å: Chain C: W.88, N.124, A.125, L.126, H.180 Chain D: F.128, S.129, F.130, D.139 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.128, D:F.130, C:N.124, C:L.126 Hydrogen bonds: C:H.180 Water bridges: C:H.180 ABA.10: 10 residues within 4Å: Chain C: F.130, D.139 Chain D: S.113, K.114, L.115, N.124, A.125, L.126, V.179, H.180 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.115, D:N.124, D:V.179 Hydrogen bonds: D:S.113, D:S.113, D:N.124, D:H.180, C:D.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocha, B.A. et al., Structural basis for both pro- and anti-inflammatory response induced by mannose-specific legume lectin from Cymbosema roseum. Biochimie (2011)

Release Date

2010-04-07

Peptides

Cymbosema roseum mannose-specific lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

Cymbosema roseum mannose-specific lectin

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