SMTL ID : 7aqz.1

Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in complex with Nanobody VSG2(NB14)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

hetero-2-2-mer

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: 16 residues within 4Å: Chain A: 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.335, A:K.314, A:S.317, A:K.333, A:K.41, A:R.48, A:S.317 Hydrophobic interactions: A:E.313 Water bridges: A:R.48, A:R.48, A:S.317 NAG-NAG-BMA-MAN.2: 15 residues within 4Å: Chain B: 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, L.337, E.338 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.48, B:L.337, B:R.48, B:S.317 Hydrophobic interactions: B:E.313 Water bridges: B:K.41, B:R.48, B:E.313, B:S.317

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

CIT.3: 11 residues within 4Å: Chain A: N.324, L.325, V.326, G.327, K.342 Chain B: K.276, E.280, K.286 Chain C: T.54, S.56, R.57 13 PLIP interactions: 6 interactions with chain B, 6 interactions with chain C, 1 interactions with chain A Water bridges: B:K.276, B:K.276, B:E.280, C:S.52, C:S.52, C:T.54 Salt bridges: B:K.276, B:K.276, B:K.286, A:K.342 Hydrogen bonds: C:T.54, C:S.56, C:R.57 CIT.4: 14 residues within 4Å: Chain A: R.43, L.47, S.50, T.344, L.347, R.351 Chain B: R.43, A.46, L.47, S.50, A.69, A.73, L.347, R.351 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.47, A:L.347 Hydrogen bonds: A:T.344, A:R.351, B:R.43, B:S.50, B:S.50 Salt bridges: A:R.43, A:R.351, A:R.351, B:R.351 CIT.7: 10 residues within 4Å: Chain A: K.276, E.280 Chain B: N.324, L.325, V.326, G.327, K.342 Chain D: S.52, T.54, S.56 7 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B, 2 interactions with chain D Salt bridges: A:K.276, A:K.276, B:K.342 Hydrogen bonds: B:L.325, D:T.54, D:S.56 Water bridges: B:G.327

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

NA.5: 4 residues within 4Å: Chain C: D.99, L.100, V.110, E.112 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.100, C:V.110, C:E.112 NA.6: 4 residues within 4Å: Chain D: D.99, L.100, V.110, E.112 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.99, D:V.110

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(NB14): 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(NB14)

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