SMTL ID : 8ux7.1

Dioclea megacarpa lectin (DmegA) complexed with X-Man

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.8, D.10, D.19, H.24, S.34 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.1, H2O.1 MN.5: 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.3, H2O.3 MN.9: 5 residues within 4Å: Chain C: E.8, D.10, D.19, H.24, S.34 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.4, H2O.4 MN.13: 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.6, H2O.6

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.6: 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.3, H2O.3 CA.10: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.10, C:D.10, C:Y.12, C:D.19, H2O.4 CA.14: 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.6, H2O.7

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.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.99 Hydrogen bonds: A:Y.12, A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:R.228 XMM.7: 8 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.99 Hydrogen bonds: B:Y.12, B:Y.12, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:R.228 XMM.11: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.99 Hydrogen bonds: C:Y.12, C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228 XMM.15: 8 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.99 Hydrogen bonds: D:Y.12, D:Y.12, D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:R.228

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: S.113, K.114, N.124, S.125, L.126, V.179, H.180 Chain C: F.130, D.139 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.180, C:D.139 GOL.12: 9 residues within 4Å: Chain A: F.130, D.139 Chain C: S.113, K.114, N.124, S.125, L.126, V.179, H.180 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:H.180, A:D.139

2 x K: POTASSIUM ION(Non-covalent)

K.8: 6 residues within 4Å: Chain B: D.28, I.29, S.31, R.33, S.34, K.35 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.31, B:R.33 K.16: 6 residues within 4Å: Chain D: D.28, I.29, S.31, R.33, S.34, K.35 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.31, D:R.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oliveira, M.V. et al., Dioclea megacarpa lectin (DmegA) complexed with X-Man. To Be Published

Release Date

2023-11-29

Peptides

Dioclea megacarpa lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dioclea megacarpa lectin