SMTL ID : 5syt.1

Crystal Structure of ZMPSTE24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: L.101, L.129, L.132, F.133, L.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.129 SO4.2: 5 residues within 4Å: Chain A: S.81, Y.84, S.85, G.138, W.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.81

1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.3: 5 residues within 4Å: Chain A: L.32, T.35, F.36, Q.39, R.43 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.35, A:F.36 Hydrogen bonds: A:Q.39 Water bridges: A:R.43, A:R.43 Salt bridges: A:R.43

1 x CXE: PENTAETHYLENE GLYCOL MONODECYL ETHER(Non-covalent)

CXE.4: 18 residues within 4Å: Chain A: F.126, L.127, A.130, T.131, L.185, T.204, N.355, S.356, C.359, F.360, L.385, L.388, L.389, F.392, Q.393, F.396, N.400 Ligands: C8E.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.127, A:A.130, A:L.385, A:L.389 Hydrogen bonds: A:N.355, A:N.400

12 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.5: 14 residues within 4Å: Chain A: L.205, S.208, L.209, V.212, H.339, H.344, T.345, N.348, I.349, S.352, Q.353, L.407, S.411, F.414 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.345, A:F.414 Hydrogen bonds: A:Q.353 C8E.6: 12 residues within 4Å: Chain A: L.132, A.135, L.136, L.139, M.164, A.167, I.168, K.170, F.171, V.172, T.174 Ligands: C8E.11 No protein-ligand interaction detected (PLIP) C8E.7: 7 residues within 4Å: Chain A: P.140, L.143, Y.144, F.147, V.148, L.160 Ligands: C8E.16 No protein-ligand interaction detected (PLIP) C8E.8: 9 residues within 4Å: Chain A: L.25, W.28, Y.31, L.32, L.83, E.86, T.87, T.90 Ligands: PEG.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.28, A:L.32 C8E.9: 11 residues within 4Å: Chain A: I.92, G.97, I.98, Y.100, L.101, F.126, A.130, F.133, L.389 Ligands: CXE.4, C8E.15 No protein-ligand interaction detected (PLIP) C8E.10: 14 residues within 4Å: Chain A: V.23, F.26, S.27, V.30, S.85, E.86, E.88, G.89, T.90, L.93, Q.393, F.394, S.397, E.401 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.88 C8E.11: 15 residues within 4Å: Chain A: S.134, A.135, G.138, L.139, S.142, T.146, Q.158, F.162, F.163, D.166, A.167, K.170, R.260, S.261 Ligands: C8E.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.260, A:R.260 Hydrogen bonds: A:A.135, A:Q.158, A:D.166, A:R.260 C8E.12: 7 residues within 4Å: Chain A: T.76, W.80, L.83, Y.84, T.87, W.141 Ligands: C8E.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.84, A:W.141 C8E.13: 12 residues within 4Å: Chain A: I.19, A.22, V.23, F.26, L.366, R.369, E.371, L.372, F.394, I.395, S.397, P.398 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.22 C8E.14: 7 residues within 4Å: Chain A: D.194, Y.195, F.197, F.361, A.364, V.365 Ligands: GOL.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.194 C8E.15: 7 residues within 4Å: Chain A: L.91, I.92, F.95, G.96, G.97, Y.100 Ligands: C8E.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.103 C8E.16: 12 residues within 4Å: Chain A: D.73, T.76, F.77, W.80, P.140, W.141, Y.144, V.148, I.149, K.152 Ligands: C8E.7, C8E.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.77, A:P.140, A:W.141, A:W.141, A:W.141, A:Y.144, A:Y.144 Hydrogen bonds: A:K.152

1 x ZN: ZINC ION(Non-covalent)

ZN.17: 5 residues within 4Å: Chain A: H.335, E.336, H.339, E.415, H.459 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.335, A:H.339, A:E.415, A:E.415, H2O.2

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 6 residues within 4Å: Chain A: I.189, K.190, F.196, F.363, I.367, T.384 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.189, A:T.384 Water bridges: A:K.190, A:K.190 GOL.19: 5 residues within 4Å: Chain A: V.365, G.368, R.369, K.370 Ligands: C8E.14 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.365, A:R.369 Water bridges: A:G.368, A:G.368, A:R.369, A:E.371

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.20: 8 residues within 4Å: Chain A: L.10, M.13, R.18, G.21, A.22, L.25, W.28 Ligands: C8E.8 No protein-ligand interaction detected (PLIP)

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

DMS.21: 9 residues within 4Å: Chain A: T.227, L.229, P.230, V.254, D.281, L.284, Y.287, S.288, V.289 No protein-ligand interaction detected (PLIP) DMS.22: 4 residues within 4Å: Chain A: K.66, L.69, K.152, H.153 No protein-ligand interaction detected (PLIP) DMS.23: 4 residues within 4Å: Chain A: H.456, Y.457, S.458, H.459 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.458, A:H.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, K.M. et al., Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors. Protein Sci. (2017)

Release Date

2016-11-02

Peptides

CAAX prenyl protease 1 homolog: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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CAAX prenyl protease 1 homolog