SMTL ID : 4z8b.1

crystal structure of a DGL mutant - H51G H131N

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.10, Y.12, P.13, N.14, D.19, H.24, R.228 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.1 CA.7: 7 residues within 4Å: Chain B: D.10, Y.12, P.13, N.14, D.19, H.24, R.228 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.4

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

MN.2: 5 residues within 4Å: Chain A: E.8, D.10, D.19, P.20, H.24 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.1 MN.8: 5 residues within 4Å: Chain B: E.8, D.10, D.19, P.20, H.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.4

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

SO4.3: 4 residues within 4Å: Chain A: T.44, G.45, K.200, S.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.201 SO4.4: 4 residues within 4Å: Chain A: Q.135, F.147, D.149, S.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.150, A:S.150, A:S.150 SO4.9: 4 residues within 4Å: Chain B: T.44, G.45, K.200, S.201 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.201 SO4.10: 4 residues within 4Å: Chain B: Q.135, F.147, D.149, S.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.150, B:S.150, B:S.150

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: L.142, Q.143, G.144, I.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.144 GOL.11: 4 residues within 4Å: Chain B: L.142, Q.143, G.144, I.221 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.144

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

XMM.6: 5 residues within 4Å: Chain A: A.58, K.59, D.78, V.79, D.80 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.59, A:K.59, A:D.78 Hydrogen bonds: A:D.80 XMM.12: 5 residues within 4Å: Chain B: A.58, K.59, D.78, V.79, D.80 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.59, B:K.59, B:D.78 Hydrogen bonds: B:D.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zamora-Caballero, S. et al., Quaternary structure of Dioclea grandiflora lectin assessed by equilibrium sedimentation and crystallographic analysis of recombinant mutants. Febs Lett. (2015)

Release Date

2015-07-22

Peptides

Lectin alpha chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lectin alpha chain