SMTL ID : 5cdv.1

Proline dipeptidase from Deinococcus radiodurans R1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.210, D.221, M.222, T.223, E.328 Ligands: PO4.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.210, A:D.221, A:M.222, A:T.223, A:E.328 MN.8: 6 residues within 4Å: Chain B: D.210, D.221, M.222, T.223, E.328 Ligands: PO4.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.210, B:D.221, B:M.222, B:T.223, B:E.328

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

NA.2: 6 residues within 4Å: Chain A: D.221, M.222, T.312, E.328, D.329, L.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.328 NA.9: 6 residues within 4Å: Chain B: D.221, M.222, T.312, E.328, D.329, L.330 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.328

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

PO4.3: 9 residues within 4Å: Chain A: F.179, D.210, D.221, T.223, H.285, H.292, E.314, E.328 Ligands: MN.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.210, A:T.223, A:E.314, A:E.328 Water bridges: A:E.314, A:E.314 Salt bridges: A:H.285, A:H.292 PO4.4: 8 residues within 4Å: Chain A: G.121, G.122, R.124, E.290, H.292, E.293, G.294 Ligands: PO4.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.122, A:H.292, A:G.294 Water bridges: A:R.124, A:R.124, A:R.124 Salt bridges: A:R.124 PO4.5: 7 residues within 4Å: Chain A: A.23, N.26, E.92, E.94, L.120, G.121 Ligands: PO4.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.26 Water bridges: A:L.116, A:L.116, A:L.120, A:R.124, A:R.124 PO4.6: 5 residues within 4Å: Chain A: V.98, E.102, R.105 Chain B: F.91, A.115 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:L.113, B:A.115 Salt bridges: A:R.105 PO4.7: 4 residues within 4Å: Chain A: R.28, T.34, G.216, G.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.34 Water bridges: A:G.216, A:G.217, A:G.217 Salt bridges: A:R.28 PO4.10: 9 residues within 4Å: Chain B: F.179, D.210, D.221, T.223, H.285, H.292, E.314, E.328 Ligands: MN.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.210, B:E.314, B:E.328 Water bridges: B:T.312 Salt bridges: B:H.285, B:H.292 PO4.11: 8 residues within 4Å: Chain B: G.121, G.122, R.124, E.290, H.292, E.293, G.294 Ligands: PO4.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.122, B:E.290, B:H.292, B:G.294 Water bridges: B:R.124, B:R.124, B:R.124 Salt bridges: B:R.124 PO4.12: 7 residues within 4Å: Chain B: A.23, N.26, E.92, E.94, L.120, G.121 Ligands: PO4.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.26, B:E.92 Water bridges: B:L.116, B:L.116, B:L.120, B:R.124, B:R.124 PO4.13: 5 residues within 4Å: Chain A: F.91, A.115 Chain B: V.98, E.102, R.105 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.102 Salt bridges: B:R.105 Water bridges: A:L.113, A:A.115 PO4.14: 4 residues within 4Å: Chain B: R.28, T.34, G.216, G.217 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.34 Water bridges: B:G.216, B:G.217, B:G.217 Salt bridges: B:R.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Proline dipeptidase from Deinococcus radiodurans R1 at 1.45 Angstrom resolution. To Be Published

Release Date

2016-08-10

Peptides

Proline dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Proline dipeptidase

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