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

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

Coordinates

PDB Format

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.15 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.81, A:H.85, A:E.182, A:E.182, ACT.15

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

3UE.2: 17 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, ACT.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.360, A:I.409, A:Y.427, A:Y.427, A:L.444, A:L.444 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.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.314, A:A.320, A:F.321, A:L.325, A:Y.357, A:L.405, A:L.441, A:L.441, A:L.444 Hydrogen bonds: A:S.324 pi-Stacking: A:F.321

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: F.187, I.193, H.197, V.211, D.215, Y.487 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.487 Water bridges: A:H.197 GOL.5: 5 residues within 4Å: Chain A: S.324, S.327, G.356, Y.357 Ligands: 3UE.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.357 GOL.6: 8 residues within 4Å: Chain A: Q.84, H.85, F.100, F.101, N.113, A.114, R.877 Ligands: ACT.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.114, A:R.877, A:R.877 Water bridges: A:H.85, A:E.157 GOL.7: 5 residues within 4Å: Chain A: S.33, E.36, K.443, G.445, N.446 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.36, A:G.445, A:N.446 GOL.8: 4 residues within 4Å: Chain A: S.694, L.697, Y.698, S.718 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.694, A:S.694, A:S.718 GOL.9: 9 residues within 4Å: Chain A: H.81, Q.84, F.115, T.116, E.182, M.183, R.192, G.213 Ligands: ACT.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.84, A:T.116, A:R.192 GOL.10: 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.13, A:Y.17, A:Y.17, A:G.246, A:L.250

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

ACT.11: 3 residues within 4Å: Chain A: K.500, Q.501, E.504 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.500 Hydrogen bonds: A:E.504 ACT.12: 5 residues within 4Å: Chain A: D.354, V.355, Y.357, N.358 Ligands: 3UE.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.354, A:D.354 ACT.13: 4 residues within 4Å: Chain A: E.191, D.350, P.353, E.686 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.686 Hydrogen bonds: A:E.191 Water bridges: A:D.354, A:N.689 ACT.14: 8 residues within 4Å: Chain A: T.549, V.944, D.948, K.949, G.950, M.951, D.952, K.963 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.549 Hydrogen bonds: A:G.950, A:M.951, A:D.952, A:H.953 ACT.15: 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.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.84 Salt bridges: A:H.81, A:H.85

2 x CA: CALCIUM ION(Non-covalent)

CA.16: 1 residues within 4Å: Chain A: N.667 No protein-ligand interaction detected (PLIP) CA.17: 2 residues within 4Å: Chain A: L.606, E.611 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.606, A:E.611, H2O.7, H2O.7

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
B

Presequence protease, mitochondrial

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