SMTL ID : 4u3e.1

Anaerobic ribonucleotide reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.614, H.618, C.625, C.628 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.614, A:H.618, A:C.625, A:C.628 ZN.6: 4 residues within 4Å: Chain B: C.614, H.618, C.625, C.628 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.614, B:H.618, B:C.625, B:C.628

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 10 residues within 4Å: Chain A: Y.132, H.134, D.135, H.137, A.519, E.520, K.521, A.522 Ligands: NA.4, ACT.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:K.521 Hydrogen bonds: A:Y.132, A:D.135, A:D.135, A:D.135, A:A.519, A:K.521, A:A.522 Water bridges: A:K.95, A:R.136, A:R.136, A:R.136, A:A.519, A:E.520, A:E.520 Salt bridges: A:H.134, A:H.134, A:H.137, A:K.521 CIT.7: 9 residues within 4Å: Chain B: Y.132, H.134, D.135, R.136, H.137, A.519, E.520, K.521, A.522 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:K.521 Hydrogen bonds: B:Y.132, B:Y.132, B:D.135, B:D.135, B:R.136, B:K.521, B:A.522 Water bridges: B:H.134, B:H.134, B:R.136, B:H.137, B:A.519, B:E.520, B:E.520 Salt bridges: B:H.134, B:H.134, B:H.137

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: S.166, E.167, T.174, Q.177, H.178 Chain B: Y.234, Q.238 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:Q.238, A:E.167, A:Q.177, A:Q.177, A:H.178 Water bridges: B:Q.230, B:Y.234, A:K.165, A:E.167 GOL.8: 7 residues within 4Å: Chain A: Q.230, Y.234, Q.238 Chain B: S.166, E.167, Q.177, H.178 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.167, B:Q.177, B:H.178, A:Q.238, A:Q.238 Water bridges: A:Y.234, A:E.294

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

NA.4: 3 residues within 4Å: Chain A: D.135 Ligands: CIT.2, ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.135, A:D.135 Water bridges: A:Y.144

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 6 residues within 4Å: Chain A: H.134, D.135, Y.144, V.391 Ligands: CIT.2, NA.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.391 Hydrogen bonds: A:Y.144 Water bridges: A:D.135, A:V.391 Salt bridges: A:H.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, Y. et al., The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-09-03

Peptides

Ribonucleoside triphosphate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside triphosphate reductase