SMTL ID : 5uph.1

Lipids bound lysosomal integral membrane protein 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: N.41, E.57, L.105, R.107, T.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.7: 9 residues within 4Å: Chain B: E.118, Q.121, L.292, N.298, S.300, I.309, Y.361 Ligands: NAG-NAG-BMA-MAN-MAN-M6D-MAN.3, NAG-NAG-BMA-MAN-MAN-M6D-MAN.3 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 7 residues within 4Å: Chain A: W.26, Y.64, L.67, Y.90, V.91, W.151, N.179 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain B: W.26, Y.64, A.89, Y.90, V.91, W.151, N.179 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- M6D- MAN: 6-O-phosphono-beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-M6D-MAN.3: 15 residues within 4Å: Chain A: E.118, Q.121, L.292, N.298, S.300, I.309, Y.361, K.363 Chain B: R.248, C.291, L.292, L.297, N.298 Ligands: NAG-NAG-BMA-MAN.7, NAG-NAG-BMA-MAN.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.363, A:K.363, A:Q.121, A:K.363, B:N.298 Salt bridges: B:R.248

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

NAG-NAG-BMA-MAN-MAN.4: 8 residues within 4Å: Chain A: Q.36, Y.38, E.58, D.335, R.355, Y.383, N.385, S.387 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.38 NAG-NAG-BMA-MAN-MAN.5: 5 residues within 4Å: Chain B: N.41, E.57, L.105, R.107, T.143 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.143 NAG-NAG-BMA-MAN-MAN.8: 8 residues within 4Å: Chain B: Q.36, Y.38, E.58, D.335, R.355, Y.383, N.385, S.387 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.38 Hydrogen bonds: B:Y.38

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 22 residues within 4Å: Chain A: V.33, D.185, V.187, E.203, V.241, V.250, V.270, L.297, M.310, F.312, T.338, F.339, V.340, I.349, A.352, A.353, K.354, R.355, F.356, E.386, V.388 Ligands: PCW.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.33, A:E.203, A:V.241, A:F.312, A:T.338, A:V.340, A:I.349, A:A.352, A:K.354, A:K.354, A:V.388 CLR.11: 23 residues within 4Å: Chain B: V.33, D.185, V.187, E.203, V.241, V.250, I.252, V.270, L.297, M.310, S.311, F.312, T.338, F.339, V.340, I.349, A.352, A.353, K.354, R.355, F.356, E.386, V.388 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.33, B:V.187, B:V.241, B:F.312, B:T.338, B:V.340, B:I.349, B:I.349, B:A.352, B:K.354, B:K.354, B:V.388

3 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.10: 29 residues within 4Å: Chain A: T.115, W.119, F.124, L.158, D.167, I.168, S.169, F.172, G.173, L.174, F.175, Y.176, E.177, K.178, T.181, P.243, D.245, C.247, V.299, C.302, K.303, N.304, A.306, I.308, M.310, F.356, I.358 Chain B: I.301 Ligands: CLR.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.124, A:E.177, A:T.181, A:A.306 Salt bridges: A:K.178, A:K.178, A:D.245, A:K.303, A:K.303 PCW.12: 28 residues within 4Å: Chain A: I.301 Chain B: T.115, W.119, F.124, L.158, D.167, I.168, S.169, F.172, G.173, L.174, F.175, Y.176, E.177, K.178, T.181, P.243, D.245, C.247, V.299, C.302, K.303, N.304, A.306, I.308, M.310, F.356, I.358 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.115, B:W.119, B:F.124, B:L.158, B:I.168, B:E.177, B:T.181, B:A.306 Salt bridges: B:K.178, B:K.178, B:D.245, B:K.303, B:K.303 PCW.13: 1 residues within 4Å: Chain B: F.242 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.242, B:F.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Conrad, K.S. et al., Lysosomal integral membrane protein-2 as a phospholipid receptor revealed by biophysical and cellular studies. Nat Commun (2017)

Release Date

2017-12-13

Peptides

Lysosome membrane protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysosome membrane protein 2