SMTL ID : 3zwf.1

Crystal structure of Human tRNase Z, short form (ELAC1).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: R.98, D.99, W.102 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.99, A:D.99 Water bridges: A:R.98 EDO.5: 7 residues within 4Å: Chain A: T.4, R.25, S.46, Q.47, L.48, F.352, V.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.47 EDO.6: 5 residues within 4Å: Chain A: M.1, D.2, R.25, E.27, G.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.1, A:E.27, A:G.28 EDO.7: 3 residues within 4Å: Chain A: R.98, Y.116 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.116, A:Y.116 EDO.8: 5 residues within 4Å: Chain A: G.38, T.41 Chain B: G.38, T.41 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.41, B:T.41 EDO.9: 7 residues within 4Å: Chain A: P.13, G.18, G.38, T.41, Q.42, K.45 Ligands: EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.37, A:T.41, A:K.45, A:K.45 Water bridges: A:A.19 EDO.14: 4 residues within 4Å: Chain B: V.122, P.123, T.124, A.125 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain B: T.4, R.25, Q.47, L.48, V.354 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.4 EDO.16: 5 residues within 4Å: Chain A: H.109 Chain B: C.128, R.181, I.182, P.183 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.109 EDO.17: 7 residues within 4Å: Chain B: D.34, H.65, L.249, G.250, D.251, E.273, H.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.34, B:D.251, B:D.251

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.64, H.65, D.251, H.311 Ligands: ZN.3, PO4.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.64, A:H.65, A:D.251, A:H.311, H2O.3 ZN.3: 6 residues within 4Å: Chain A: H.60, H.62, H.180, D.251 Ligands: ZN.2, PO4.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.60, A:H.62, A:H.180, A:D.251, H2O.3 ZN.10: 6 residues within 4Å: Chain B: H.60, H.62, H.180, D.251 Ligands: ZN.11, PO4.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.60, B:H.62, B:H.180, B:D.251, H2O.8 ZN.11: 6 residues within 4Å: Chain B: D.64, H.65, D.251, H.311 Ligands: ZN.10, PO4.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.64, B:H.65, B:D.251, B:H.311, H2O.8

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 10 residues within 4Å: Chain A: A.11, H.62, D.64, H.180, R.181, D.251, H.289, H.311 Ligands: ZN.2, ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.11 Salt bridges: A:H.62, A:H.180, A:R.181, A:H.289, A:H.311 PO4.12: 10 residues within 4Å: Chain B: A.11, H.62, D.64, H.180, R.181, D.251, H.289, H.311 Ligands: ZN.10, ZN.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.11 Salt bridges: B:H.62, B:H.180, B:R.181, B:H.289, B:H.311

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 4 residues within 4Å: Chain B: L.43, M.44, S.46, L.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allerston, C.K. et al., Crystal Structure of Human Trnase Z, Short Form (Elac1). To be Published

Release Date

2011-08-10

Peptides

ZINC PHOSPHODIESTERASE ELAC PROTEIN 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ZINC PHOSPHODIESTERASE ELAC PROTEIN 1