SMTL ID : 6p8c.1

2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: R.72, R.91, L.92, H.95 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: R.72, R.91, L.92, H.95 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: H.169, E.174 No protein-ligand interaction detected (PLIP) GOL.3: 7 residues within 4Å: Chain A: R.73, C.75, D.76, G.102, D.103, N.104, P.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.76, A:N.104 GOL.4: 5 residues within 4Å: Chain A: R.67, R.233, Y.235, E.244 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.235, A:Y.235, A:E.244 Water bridges: A:R.67 GOL.5: 4 residues within 4Å: Chain A: I.39, E.196, R.198 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.196 Water bridges: A:R.67, A:R.198

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: R.209, A.211 Chain B: R.209 5 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain A, 1 interactions with chain B Metal complexes: H2O.2, H2O.3, H2O.8, A:R.209, B:R.209

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.7: 24 residues within 4Å: Chain A: A.42, A.43, I.50, A.51, G.81, I.82, N.83, T.84, D.88, V.110, D.111, S.112, R.115, R.158, V.159, L.161, E.179, G.180, G.181, S.182, T.183, L.184, S.187, R.212 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:I.50, A:T.84 Hydrogen bonds: A:A.43, A:A.43, A:G.81, A:I.82, A:N.83, A:N.83, A:T.84, A:D.88, A:S.112, A:S.112, A:S.112, A:V.159, A:V.159, A:G.180, A:G.181, A:S.182, A:T.183, A:T.183, A:T.183, A:L.184, A:S.187 Water bridges: A:M.113, A:R.158, A:T.183 Salt bridges: A:R.115, A:R.212 pi-Cation interactions: A:R.158 NAP.9: 25 residues within 4Å: Chain B: A.42, A.43, I.50, A.51, G.81, I.82, N.83, T.84, A.87, D.88, V.110, D.111, S.112, R.115, R.158, V.159, L.161, E.179, G.180, G.181, S.182, T.183, L.184, S.187, R.212 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.50, B:T.84 Hydrogen bonds: B:A.43, B:A.43, B:G.81, B:I.82, B:N.83, B:N.83, B:T.84, B:D.88, B:S.112, B:S.112, B:M.113, B:V.159, B:V.159, B:G.180, B:G.181, B:S.182, B:T.183, B:T.183, B:T.183, B:L.184, B:S.187 Water bridges: B:R.115, B:R.115 Salt bridges: B:R.115, B:R.212 pi-Cation interactions: B:R.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carbone, V. et al., The Crystal Structure of 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus. To Be Published

Release Date

2020-06-10

Peptides

2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase