SMTL ID : 1s4o.1

Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: binary complex with GDP/Mn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NDG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NDG-BMA-MAN-MAN-MAN-MAN-MAN.1: 3 residues within 4Å: Chain A: N.103, K.106, E.109 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.109, A:E.109 Hydrogen bonds: A:N.103, A:E.109

1 x NAG- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG.2: 4 residues within 4Å: Chain B: N.103, T.105, K.106, E.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.103, B:E.109

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

MN.3: 3 residues within 4Å: Chain A: E.153, H.294 Ligands: GDP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.153, A:H.294, H2O.2, H2O.10 MN.8: 3 residues within 4Å: Chain B: E.153, H.294 Ligands: GDP.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.153, B:H.294, H2O.20, H2O.20

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

CL.4: 2 residues within 4Å: Chain A: S.97, Y.98 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: Q.323, G.324, Y.325 Chain B: I.119, Y.120 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: I.119, Y.120 Chain B: Q.323, G.324, Y.325 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: S.97, Y.98 Ligand excluded by PLIP

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.5: 15 residues within 4Å: Chain A: L.34, V.35, R.36, E.39, N.66, D.67, W.96, Y.120, S.125, Y.126, M.129, E.153, P.154, H.294 Ligands: MN.3 24 PLIP interactions: 22 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.36, A:E.39, A:N.66, A:D.67, A:Y.120, A:Y.120 Water bridges: A:L.34, A:L.34, A:R.36, A:R.36, A:N.66, A:D.67, A:D.67, A:W.96, A:S.125, A:Y.126, A:N.233, A:N.233, B:N.318, B:N.318 Salt bridges: A:R.36, A:D.67, A:H.294 pi-Cation interactions: A:R.36 GDP.11: 15 residues within 4Å: Chain B: L.34, V.35, R.36, E.39, N.66, D.67, W.96, Y.120, S.125, Y.126, M.129, E.153, P.154, H.294 Ligands: MN.8 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:V.35, B:R.36, B:R.36, B:E.39, B:N.66, B:D.67, B:Y.120, B:Y.126 Water bridges: B:L.34, B:N.66, B:D.67, B:D.67, B:Y.120, B:Y.120, B:Y.120, B:S.125, B:S.125, B:Y.126, B:V.152, B:N.233 Salt bridges: B:D.67, B:H.294 pi-Cation interactions: B:R.36

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 9 residues within 4Å: Chain A: G.317, Q.323, N.342, K.345, F.346, E.348 Chain B: Y.120, S.123, Y.126 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.123, A:N.342 Water bridges: B:R.36, B:S.123, B:S.125, B:S.125 EPE.12: 10 residues within 4Å: Chain A: R.36, Y.120, S.123, S.125, Y.126 Chain B: G.317, Q.323, K.345, F.346, E.348 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.345, B:E.348 Hydrogen bonds: A:R.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lobsanov, Y.D. et al., Structure of Kre2p/Mnt1p: A YEAST {alpha}1,2-MANNOSYLTRANSFERASE INVOLVED IN MANNOPROTEIN BIOSYNTHESIS. J.Biol.Chem. (2004)

Release Date

2004-05-04

Peptides

Glycolipid 2-alpha-mannosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycolipid 2-alpha-mannosyltransferase

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