SMTL ID : 4fco.2 (1 other biounit)

Crystal structure of bace1 with its inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: Y.91, Q.93, Q.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.91, A:Y.91, A:Q.93, A:Q.95 SO4.2: 1 residues within 4Å: Chain A: R.101 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.101, A:R.136, A:R.136 Salt bridges: A:R.101 SO4.3: 6 residues within 4Å: Chain A: S.62, P.63, S.98 Chain B: F.39, H.185, P.187 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.62, A:S.98, B:G.217 Salt bridges: B:H.185 SO4.7: 3 residues within 4Å: Chain B: Y.91, Q.93, Q.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.91, B:Q.93, B:Q.95 SO4.8: 1 residues within 4Å: Chain B: R.101 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.101, B:R.136, B:R.136 Salt bridges: B:R.101 SO4.9: 6 residues within 4Å: Chain A: F.39, H.185, P.187 Chain B: S.62, P.63, S.98 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.217, B:S.62, B:S.98 Salt bridges: A:H.185

2 x 0U4: N-[(2S,3R)-4-{[2-(1-BENZYLPIPERIDIN-4-YL)ETHYL]AMINO}-3-HYDROXY-1-PHENYLBUTAN-2-YL]-5-[METHYL(METHYLSULFONYL)AMINO]-N'-[(1R)-1-PHENYLETHYL]BENZENE-1,3-DICARBOXAMIDE(Non-covalent)

0U4.4: 28 residues within 4Å: Chain A: G.51, Q.52, G.53, L.70, D.72, G.74, S.75, Y.111, T.112, Q.113, F.148, W.155, I.158, Y.238, K.264, I.266, D.268, S.269, G.270, T.271, T.272, N.273, R.275, R.347, S.365, T.369, A.375 Ligands: URE.6 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.70, A:L.70, A:Y.111, A:Y.111, A:Q.113, A:F.148, A:F.148, A:W.155, A:I.158, A:I.266, A:T.369, A:A.375 Hydrogen bonds: A:D.72, A:T.112, A:Q.113, A:Q.113, A:D.268, A:G.270, A:G.270, A:T.271, A:T.272, A:T.272, A:N.273, A:S.365 Water bridges: A:R.275 0U4.10: 28 residues within 4Å: Chain B: G.51, Q.52, G.53, L.70, D.72, G.74, S.75, Y.111, T.112, Q.113, F.148, W.155, I.158, Y.238, K.264, I.266, D.268, S.269, G.270, T.271, T.272, N.273, R.275, R.347, S.365, T.369, A.375 Ligands: URE.12 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:L.70, B:L.70, B:Y.111, B:Y.111, B:Q.113, B:F.148, B:F.148, B:W.155, B:I.158, B:I.266, B:T.369, B:A.375 Hydrogen bonds: B:D.72, B:T.112, B:T.112, B:Q.113, B:Q.113, B:D.268, B:G.270, B:G.270, B:T.272, B:N.273, B:S.365, B:T.369 Water bridges: B:T.272, B:T.272, B:R.275

4 x URE: UREA(Non-functional Binders)

URE.5: 1 residues within 4Å: Chain A: F.87 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.147, A:K.147, A:K.147 URE.6: 1 residues within 4Å: Ligands: 0U4.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.275, A:Q.366 URE.11: 1 residues within 4Å: Chain B: F.87 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.147, B:K.147, B:K.147 URE.12: 1 residues within 4Å: Ligands: 0U4.10 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.275, B:Q.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y.C. et al., Flexibility of the Flap in the Active Site of BACE1 as Revealed by Crystal Structures and MD simulations. To be Published (2012)

Release Date

2013-05-29

Peptides

Beta-secretase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-secretase 1

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