SMTL ID : 2y1h.1

Crystal structure of the human TatD-domain protein 3 (TATDN3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.68, E.105, H.145, H.168 Ligands: ZN.2, PO4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.105, A:H.145, A:H.168 ZN.2: 7 residues within 4Å: Chain A: H.10, H.12, E.105, H.168, D.216 Ligands: ZN.1, PO4.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.10, A:H.12, A:E.105, A:D.216 ZN.5: 7 residues within 4Å: Chain B: H.10, H.12, E.105, H.168, D.216 Ligands: ZN.6, PO4.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.10, B:H.12, B:E.105, B:D.216 ZN.6: 6 residues within 4Å: Chain B: H.68, E.105, H.145, H.168 Ligands: ZN.5, PO4.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.105, B:H.145, B:H.168

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

PO4.3: 11 residues within 4Å: Chain A: H.10, H.12, E.42, H.68, E.105, H.145, R.147, H.168, D.216 Ligands: ZN.1, ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.147 Water bridges: A:E.42 Salt bridges: A:H.12, A:H.68, A:H.145, A:H.168 PO4.7: 10 residues within 4Å: Chain B: H.10, H.12, E.42, H.68, E.105, H.145, H.168, D.216 Ligands: ZN.5, ZN.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.42 Salt bridges: B:H.12, B:H.68, B:H.145, B:H.168

2 x NI: NICKEL (II) ION(Non-covalent)

NI.4: 3 residues within 4Å: Chain A: R.227, E.229 Chain B: E.223 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.223, B:E.223, A:E.229, H2O.1 NI.8: 3 residues within 4Å: Chain A: E.223 Chain B: R.227, E.229 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.223, A:E.223, B:E.229, H2O.2, H2O.2

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

EDO.9: 3 residues within 4Å: Chain B: D.23, R.56, Y.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.56, B:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muniz, J.R.C. et al., Crystal Structure of the Human Tatd-Domain Protein 3 (Tatdn3). To be Published

Release Date

2010-12-29

Peptides

PUTATIVE DEOXYRIBONUCLEASE TATDN3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PUTATIVE DEOXYRIBONUCLEASE TATDN3