SMTL ID : 3zkn.1 (1 other biounit)

BACE2 FAB INHIBITOR COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x WZV: 5-(2,2,2-Trifluoro-ethoxy)-pyridine-2-carboxylic acid [3-((S)-2-amino-1,4-dimethyl-6-oxo-1,4,5,6-tetrahydro-pyrimidin-4-yl)-phenyl]-amide(Non-covalent)

WZV.1: 14 residues within 4Å: Chain A: L.34, D.36, G.38, S.39, Y.75, Q.77, N.111, F.112, L.114, W.119, I.122, D.229, G.231, T.232 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.34, A:Y.75, A:Y.75, A:N.111, A:F.112, A:L.114, A:W.119 Hydrogen bonds: A:Y.75, A:N.111 Water bridges: A:D.229 Salt bridges: A:D.36, A:D.229

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 6 residues within 4Å: Chain A: P.256, F.262, Q.267, L.268, C.270, W.271 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:F.262, A:W.271

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: E.86, L.100, V.101, N.102, E.138, S.143, Q.147 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.102, A:N.102, A:N.102, A:E.138, A:E.138, A:S.143, A:Q.147 Water bridges: A:K.67 Salt bridges: A:K.67 SO4.4: 6 residues within 4Å: Chain A: T.76, R.236, S.327, T.328, N.329, A.330 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.76, A:T.76, A:S.327, A:T.328, A:T.328, A:N.329, A:A.330 Salt bridges: A:R.236 SO4.5: 4 residues within 4Å: Chain B: P.192, S.193, S.195, K.212 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.195 Salt bridges: B:K.212

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain B: R.38, K.43, E.46, A.62, F.63, R.66 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.38, B:K.43, B:A.62, B:R.66 Water bridges: B:Q.86, B:Q.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banner, D.W. et al., Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-05-29

Peptides

BETA-SECRETASE 2: A
FAB HEAVY CHAIN: B
FAB LIGHT CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

BETA-SECRETASE 2

FAB HEAVY CHAIN

FAB LIGHT CHAIN

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