SMTL ID : 7aqx.1

Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in complex with Nanobody VSG2(NB9)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG-NAG-BMA.1: 13 residues within 4Å: Chain A: K.38, K.41, M.42, A.45, R.48, Y.72, F.261, N.263, E.313, I.316, S.317, G.335, E.336 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.336, A:R.48, A:E.313, A:S.317 Hydrophobic interactions: A:E.313 Hydrogen bonds: A:R.48, A:S.317

1 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.2: 16 residues within 4Å: Chain B: K.38, K.41, M.42, A.45, R.48, Y.72, F.261, N.263, E.313, K.314, I.316, S.317, E.318, K.333, G.335, E.336 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.335, B:R.48, B:S.317, B:G.335, B:K.314, B:E.318, B:K.333 Hydrophobic interactions: B:E.313 Water bridges: B:R.48, B:R.48, B:S.317

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 15 residues within 4Å: Chain A: R.43, A.46, L.47, S.50, A.69, A.73, L.347, R.351 Chain B: R.43, A.46, L.47, A.73, T.344, L.347, R.351 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.73 Hydrogen bonds: A:R.43, A:S.50, A:S.50 Salt bridges: A:R.351, B:R.43, B:R.351, B:R.351

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain C: D.99, L.100, E.109, E.111 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.100, C:E.111 Water bridges: C:S.108, C:E.109 NA.5: 4 residues within 4Å: Chain D: D.99, L.100, E.109, E.111 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.100, D:E.111 Water bridges: D:E.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hempelmann, A. et al., Nanobody-mediated macromolecular crowding induces membrane fission and remodeling in the African trypanosome. Cell Rep (2021)

Release Date

2021-11-03

Peptides

Variant surface glycoprotein MITAT 1.2: AB
Nanobody VSG2(NB9): CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Variant surface glycoprotein MITAT 1.2

Nanobody VSG2(NB9)

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