SMTL ID : 3kas.1

Machupo virus GP1 bound to human transferrin receptor 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-FUC.1: 4 residues within 4Å: Chain B: V.42, N.52, N.84, T.86 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:N.172, A:N.172 Hydrogen bonds: B:T.86 NAG-NAG-FUC.14: 4 residues within 4Å: Chain D: V.42, N.52, N.84, T.86 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.172, C:N.172

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN.2: 11 residues within 4Å: Chain A: E.230 Chain B: L.36, Q.94, N.96, S.98, A.100, D.101, D.102, G.128, K.129, Y.132 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.100 NAG-NAG-BMA-MAN-MAN-MAN-MAN.15: 11 residues within 4Å: Chain C: E.230 Chain D: L.36, Q.94, N.96, S.98, A.100, D.101, D.102, G.128, K.129, Y.132 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.100

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

NAG.3: 1 residues within 4Å: Chain A: N.131 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: N.607, T.609, L.610 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.609 Water bridges: A:N.607 NAG.10: 3 residues within 4Å: Chain B: N.13, S.15, F.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.13 NAG.11: 5 residues within 4Å: Chain B: N.55, Q.137, C.138, G.139, D.140 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.137 Hydrogen bonds: B:N.55, B:G.139, B:D.140 NAG.16: 1 residues within 4Å: Chain C: N.131 No protein-ligand interaction detected (PLIP) NAG.17: 3 residues within 4Å: Chain C: N.607, T.609, L.610 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.607 NAG.23: 3 residues within 4Å: Chain D: N.13, S.15, F.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.13 NAG.24: 5 residues within 4Å: Chain D: N.55, Q.137, C.138, G.139, D.140 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Q.137 Hydrogen bonds: D:N.55, D:G.139, D:D.140

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 4 residues within 4Å: Chain A: L.2, Y.3, W.4, H.483 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.4 Salt bridges: A:H.483 PO4.6: 8 residues within 4Å: Chain A: D.280, H.281, K.552, D.556 Chain C: K.553, D.556, R.560 Ligands: PO4.19 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:D.280, A:L.356, A:D.556, C:K.553 Salt bridges: A:H.281, A:K.552, C:R.560 Water bridges: C:K.553, C:R.560, C:R.560 PO4.7: 7 residues within 4Å: Chain A: K.375, V.376, S.377, N.419, S.434, F.435, C.436 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.377, A:S.377, A:S.434 Water bridges: A:N.419, A:N.419 PO4.8: 2 residues within 4Å: Chain A: W.4, N.392 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.388, A:N.392 Salt bridges: A:K.480 PO4.12: 5 residues within 4Å: Chain B: D.145, G.148, V.149, N.150, H.151 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.145, B:D.145, B:D.145, B:G.148, B:N.150, B:N.150, B:H.151 Water bridges: B:V.149 Salt bridges: B:H.151 PO4.13: 5 residues within 4Å: Chain B: K.99, K.108, R.111, R.115, D.123 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:K.99, B:K.108, B:R.111, B:R.115 PO4.18: 4 residues within 4Å: Chain C: L.2, Y.3, W.4, H.483 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.4 Salt bridges: C:H.483 PO4.19: 8 residues within 4Å: Chain A: K.553, D.556, R.560 Chain C: D.280, H.281, K.552, D.556 Ligands: PO4.6 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:L.356, C:D.556, A:K.553, A:D.556 Salt bridges: C:H.281, C:K.552, A:R.560 Water bridges: A:K.553, A:R.560, A:R.560 PO4.20: 7 residues within 4Å: Chain C: K.375, V.376, S.377, N.419, S.434, F.435, C.436 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.377, C:S.377, C:S.434 Water bridges: C:N.419, C:N.419 PO4.21: 2 residues within 4Å: Chain C: W.4, N.392 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.388, C:N.392 Salt bridges: C:K.480 PO4.25: 5 residues within 4Å: Chain D: D.145, G.148, V.149, N.150, H.151 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.145, D:D.145, D:G.148, D:N.150, D:N.150, D:H.151 Water bridges: D:V.149 Salt bridges: D:H.151 PO4.26: 5 residues within 4Å: Chain D: K.99, K.108, R.111, R.115, D.123 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.123 Salt bridges: D:K.99, D:K.108, D:R.111, D:R.115

2 x K: POTASSIUM ION(Non-covalent)

K.9: 4 residues within 4Å: Chain A: L.2, F.322, Q.323, H.483 No protein-ligand interaction detected (PLIP) K.22: 4 residues within 4Å: Chain C: L.2, F.322, Q.323, H.483 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abraham, J. et al., Structural basis for receptor recognition by New World hemorrhagic fever arenaviruses. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-03-09

Peptides

Transferrin receptor protein 1: AC
Glycoprotein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Transferrin receptor protein 1

Glycoprotein

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