SMTL ID : 2dur.1 (1 other biounit)

Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man2-bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 9 residues within 4Å: Chain A: S.48, E.50, D.83, N.118, H.142, T.211, G.212, D.213, L.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.50 Water bridges: A:S.48, A:S.48, A:E.50

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.114, Y.116, N.118, D.145 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.114, A:D.114, A:Y.116, A:D.145, H2O.1

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain A: R.8, S.11, L.12, I.13, Y.16, Q.17, W.27 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.161, D.162, H.163 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: E.46, R.47 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: T.180, D.181, L.182, K.189 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: N.118, S.143 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: M.132, V.133, L.138, W.148, T.149, L.151, F.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.133, A:V.133, A:T.149 GOL.9: 3 residues within 4Å: Chain A: R.91, G.202, Y.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.202 Water bridges: A:R.91, A:R.91

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Satoh, T. et al., Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36. J.Biol.Chem. (2007)

Release Date

2007-07-24

Peptides

Vesicular integral-membrane protein VIP36: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vesicular integral-membrane protein VIP36

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