SMTL ID : 4s2t.1

Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x 01B- PRO- PRO- ALA: apstatin(Non-covalent)

01B-PRO-PRO-ALA.1: 20 residues within 4Å: Chain A: Y.66, D.99, R.101, F.401, D.402, I.404, H.415, K.417, D.436, D.447, H.506, G.507, G.509, H.510, H.519, E.545, R.557, E.559 Ligands: ZN.3, ZN.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.101, A:F.401, A:F.401, A:I.404, A:H.506, A:H.510 Hydrogen bonds: A:R.101, A:D.447, A:D.447, A:G.507 Water bridges: A:H.527 pi-Stacking: A:H.415 01B-PRO-PRO-ALA.2: 20 residues within 4Å: Chain B: Y.66, D.99, R.101, F.401, D.402, I.404, H.415, K.417, D.436, D.447, H.506, G.507, G.509, H.510, H.519, E.545, R.557, E.559 Ligands: ZN.8, ZN.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.101, B:F.401, B:F.401, B:I.404, B:H.506, B:H.510 Hydrogen bonds: B:R.101, B:D.436, B:D.447, B:G.507 Water bridges: B:H.527 pi-Stacking: B:H.415

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: F.401, D.436, D.447, T.449, E.559 Ligands: 01B-PRO-PRO-ALA.1, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.436, A:D.436, A:D.447, A:E.559 ZN.4: 6 residues within 4Å: Chain A: D.447, H.510, E.545, E.559 Ligands: 01B-PRO-PRO-ALA.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.447, A:H.510, A:E.545, A:E.559 ZN.8: 7 residues within 4Å: Chain B: F.401, D.436, D.447, T.449, E.559 Ligands: 01B-PRO-PRO-ALA.2, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.436, B:D.436, B:D.447, B:E.559 ZN.9: 6 residues within 4Å: Chain B: D.447, H.510, E.545, E.559 Ligands: 01B-PRO-PRO-ALA.2, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.447, B:H.510, B:E.545, B:E.559

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

SO4.5: 6 residues within 4Å: Chain A: N.209, L.210, K.213, L.333, V.334, A.337 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.337, A:A.337 SO4.6: 7 residues within 4Å: Chain A: Y.562, F.579, K.580, S.581, W.604, Y.608, R.611 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.581, A:W.604 Salt bridges: A:R.611 SO4.7: 5 residues within 4Å: Chain A: Q.105, N.108, Q.109, L.413, Y.416 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.108, A:Q.109 SO4.10: 4 residues within 4Å: Chain B: P.146, S.170, Y.316, A.317 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.170, B:S.320, B:S.320 SO4.11: 7 residues within 4Å: Chain B: K.206, N.209, L.210, K.213, L.333, V.334, A.337 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.209, B:A.337, B:A.337 SO4.12: 4 residues within 4Å: Chain B: Q.105, N.108, Q.109, L.413 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.108, B:Q.109 SO4.13: 6 residues within 4Å: Chain B: F.579, K.580, S.581, W.604, Y.608, R.611 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.581 Salt bridges: B:R.611

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iyer, S. et al., Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site. FEBS Open Bio (2015)

Release Date

2015-04-22

Peptides

Protein APP-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
Q

Protein APP-1

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