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

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

Coordinates

PDB Format Compare

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   PDBe-KB   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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