SMTL ID : 4rpu.1 (1 other biounit)

Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.81, H.85, E.182 Ligands: ACT.17 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.81, A:H.85, A:E.182, A:E.182

2 x 3UE: [4-(DIPHENYLMETHYL)PIPERAZIN-1-YL](3-METHYL-4-NITROPHENYL)METHANONE

3UE.2: 16 residues within 4Å: Chain A: L.37, F.321, Y.357, N.358, G.359, Y.360, I.409, Q.412, M.413, F.420, M.423, L.424, Y.427, S.430, L.444 Ligands: 3UE.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.360, A:I.409, A:F.420, A:Y.427, A:Y.427, A:L.444, A:L.444 Water bridges: A:Y.360 pi-Cation interactions: A:Y.427 3UE.3: 22 residues within 4Å: Chain A: I.314, T.317, A.320, F.321, S.324, L.325, S.328, Y.357, G.359, L.405, K.408, I.409, Q.412, Y.427, S.430, C.431, E.440, L.441, L.444, Q.447 Ligands: 3UE.2, GOL.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.314, A:A.320, A:F.321, A:Y.357, A:L.405, A:L.441, A:L.441, A:L.444, A:Q.447 pi-Stacking: A:F.321

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: S.324, S.327, S.328, G.356, Y.357 Ligands: 3UE.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.324, A:Y.357 GOL.5: 4 residues within 4Å: Chain A: F.187, H.197, Y.487, Q.491 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.487, A:Q.491 Water bridges: A:H.197, A:H.197, A:Y.487 GOL.6: 9 residues within 4Å: Chain A: Q.84, H.85, L.88, F.100, F.101, N.113, E.157, R.877 Ligands: ACT.17 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.84, A:H.85, A:N.113, A:R.877 Water bridges: A:Y.883, A:Y.883 GOL.7: 5 residues within 4Å: Chain A: E.398, D.400, R.401, R.610, E.611 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.610 GOL.8: 5 residues within 4Å: Chain A: K.831, I.906, K.1004, D.1008, W.1011 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.1004 GOL.9: 6 residues within 4Å: Chain A: G.622, M.623, S.624, S.646, S.647, L.648 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.624 GOL.10: 4 residues within 4Å: Chain A: T.72, M.74, H.234, S.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.72, A:S.271 GOL.11: 11 residues within 4Å: Chain A: A.10, R.13, Y.17, H.55, A.57, G.246, N.247, F.248, P.249, L.250, E.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.246, A:L.250 GOL.12: 9 residues within 4Å: Chain A: H.81, Q.84, F.115, T.116, E.182, M.183, R.192, G.213 Ligands: ACT.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.81, A:T.116, A:R.192 GOL.13: 5 residues within 4Å: Chain A: S.694, L.697, Y.698, I.701, S.718 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.694, A:S.718 GOL.14: 2 residues within 4Å: Chain A: D.552, E.770 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.552

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.15: 2 residues within 4Å: Chain A: F.38, Q.416 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.58 ACT.16: 7 residues within 4Å: Chain A: E.191, D.350, F.351, S.352, P.353, V.355, Q.371 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.355 Hydrogen bonds: A:D.350, A:Q.371 Water bridges: A:N.689, A:N.689 ACT.17: 10 residues within 4Å: Chain A: H.81, Q.84, H.85, N.113, A.114, E.182, Y.883 Ligands: ZN.1, GOL.6, GOL.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.84, A:Q.84, A:Y.883 Salt bridges: A:H.81, A:H.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mo, S.M. et al., Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60. TO BE PUBLISHED

Release Date

2015-12-09

Peptides

Presequence protease, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Presequence protease, mitochondrial

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