SMTL ID : 6d05.1

Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 2.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

NAG-NAG.1: 4 residues within 4Å: Chain A: F.86, N.216, F.220, E.282 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.626, T.628, L.629 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: F.86, N.216, F.220, E.282 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.86 NAG-NAG.4: 3 residues within 4Å: Chain B: N.626, T.628, L.629 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.432, K.433, S.434 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: N.432, K.433, S.434 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: T.209, F.212, P.213, E.364, E.367 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.209, A:T.209, A:F.212, A:E.364, A:E.367 CA.9: 4 residues within 4Å: Chain B: T.209, F.212, E.364, E.367 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.209, B:T.209, B:F.212, B:E.364, B:E.367

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

NAG.8: 1 residues within 4Å: Chain A: N.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.150 NAG.10: 1 residues within 4Å: Chain B: N.150 No protein-ligand interaction detected (PLIP) NAG.15: 1 residues within 4Å: Chain C: N.630 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.630 NAG.20: 2 residues within 4Å: Chain D: H.625, N.630 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:H.625

4 x FE: FE (III) ION(Non-covalent)

FE.11: 7 residues within 4Å: Chain C: D.411, Y.445, T.476, Y.536, H.604, R.651 Ligands: CO3.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:Y.445, C:Y.536, C:H.604 FE.13: 6 residues within 4Å: Chain C: D.82, Y.114, S.144, Y.207, H.268 Ligands: CO3.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.82, C:Y.114, C:Y.207, C:H.268 FE.16: 7 residues within 4Å: Chain D: D.411, Y.445, T.476, Y.536, H.604, R.651 Ligands: CO3.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:Y.445, D:Y.536, D:H.604 FE.18: 6 residues within 4Å: Chain D: D.82, Y.114, S.144, Y.207, H.268 Ligands: CO3.19 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.82, D:Y.114, D:Y.207, D:H.268

4 x CO3: CARBONATE ION(Non-functional Binders)

CO3.12: 10 residues within 4Å: Chain C: D.411, Y.445, T.471, R.475, T.476, A.477, G.478, Y.536, H.604 Ligands: FE.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.475, C:T.476 CO3.14: 9 residues within 4Å: Chain C: D.82, Y.114, R.143, S.144, A.145, G.146, Y.207, H.268 Ligands: FE.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.144, C:A.145, C:G.146 CO3.17: 10 residues within 4Å: Chain D: D.411, Y.445, T.471, R.475, T.476, A.477, G.478, Y.536, H.604 Ligands: FE.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.475, D:T.476 CO3.19: 10 residues within 4Å: Chain D: D.82, Y.114, T.139, R.143, S.144, A.145, G.146, Y.207, H.268 Ligands: FE.18 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.144, D:A.145, D:G.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gruszczyk, J. et al., Cryo-EM structure of an essential Plasmodium vivax invasion complex. Nature (2018)

Release Date

2018-06-20

Peptides

Transferrin receptor protein 1: AB
Serotransferrin: CD
Reticulocyte binding protein 2, putative: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Transferrin receptor protein 1

Serotransferrin

Reticulocyte binding protein 2, putative

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