SMTL ID : 5lgd.1

The CIDRa domain from MCvar1 PfEMP1 bound to CD36

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG-MAN.1: 9 residues within 4Å: Chain A: Q.64, W.66, Q.87, E.366, R.386, W.415, N.417, T.419 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.66, A:W.415 Hydrogen bonds: A:E.366, A:E.366

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

NAG.2: 7 residues within 4Å: Chain A: H.242, C.243, M.245, N.247, Q.265, S.274, F.312 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.312 Hydrogen bonds: A:H.242, A:H.242, A:N.247, A:Q.265 NAG.3: 4 residues within 4Å: Chain A: R.234, N.235, S.241, H.242 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.234 Hydrogen bonds: A:N.235, A:N.235, A:S.241 NAG.4: 5 residues within 4Å: Chain A: A.120, I.121, R.176, W.180, N.205 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.180 Hydrogen bonds: A:R.176, A:R.176, A:N.205 Water bridges: A:A.120, A:N.205 NAG.5: 4 residues within 4Å: Chain A: T.130, A.132, D.133, N.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.132 NAG.6: 3 residues within 4Å: Chain A: Q.74, E.75, N.79 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.74 Hydrogen bonds: A:N.79 NAG.7: 2 residues within 4Å: Chain A: N.102, L.115 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.115 NAG.8: 3 residues within 4Å: Chain A: N.220, S.222, K.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.220 NAG.9: 1 residues within 4Å: Chain A: N.321 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.321

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.10: 14 residues within 4Å: Chain A: L.140, A.141, A.144, I.148, L.187, V.198, L.200, F.201, D.270, K.334, R.337, V.339, I.341, V.389 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.140, A:L.140, A:A.144, A:L.187, A:V.198, A:V.198, A:L.200, A:F.201, A:D.270, A:K.334, A:V.339, A:V.389, A:V.389 Hydrogen bonds: A:R.337 PLM.11: 15 residues within 4Å: Chain A: T.57, T.59, A.251, A.252, F.266, S.268, L.295, S.342, T.369, L.371, T.380, F.383, K.385, R.386, L.387 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.57, A:T.59, A:A.251, A:A.252, A:F.266, A:L.295, A:T.369, A:L.371, A:F.383, A:F.383, A:F.383, A:K.385 Water bridges: A:T.369

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 3 residues within 4Å: Chain A: Q.171, V.172, R.173 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.172 GOL.13: 5 residues within 4Å: Chain A: S.160, L.161, K.164 Chain B: D.93, E.97 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.160, A:S.160, B:D.93 GOL.14: 5 residues within 4Å: Chain A: E.365, E.366, R.386 Ligands: NAG-NAG-MAN.1, NAG-NAG-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.386 GOL.15: 7 residues within 4Å: Chain A: I.226, G.248, T.249, F.254, V.263, L.264, Q.265 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.249, A:Q.265, A:Q.265, A:Q.265 GOL.17: 4 residues within 4Å: Chain B: D.105, N.107, E.108, R.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.107, B:R.111

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.16: 8 residues within 4Å: Chain A: I.318, K.320, D.352, V.353, P.356, N.408, Y.409, I.410 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.320, A:S.324, A:S.324, A:D.352, A:D.352, A:N.408, A:I.410 Water bridges: A:V.353 TRS.18: 5 residues within 4Å: Chain B: D.21, K.24, W.25, E.28, H.29 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.21, B:D.21, B:H.29 Water bridges: B:H.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, F.L. et al., The structural basis for CD36 binding by the malaria parasite. Nat Commun (2016)

Release Date

2016-08-31

Peptides

Platelet glycoprotein 4: A
PfEMP1 variant 1 of strain MC: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Platelet glycoprotein 4

PfEMP1 variant 1 of strain MC