SMTL ID : 5olk.1

Crystal structure of the ATP-cone-containing NrdB from Leeuwenhoekiella blandensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

8 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 15 residues within 4Å: Chain A: I.12, K.14, R.15, P.21, F.22, V.23, K.26, I.27, A.30, V.71, V.74, Q.75, Y.94 Ligands: DTP.2, MG.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.27, A:V.74 Hydrogen bonds: A:P.21, A:V.23, A:Q.75, A:Y.94 Salt bridges: A:K.14, A:K.14, A:K.14, A:R.15 DTP.2: 14 residues within 4Å: Chain A: R.15, A.30, N.33, A.34, A.37, Q.75, A.93, Y.94, Y.97, R.98, R.101, R.105 Ligands: DTP.1, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.94, A:Y.97 Hydrogen bonds: A:Q.75, A:Y.97, A:R.101 Water bridges: A:R.15, A:R.105, A:R.105 Salt bridges: A:R.15, A:R.15, A:R.105, A:R.105 pi-Stacking: A:Y.97, A:Y.97 DTP.7: 15 residues within 4Å: Chain B: I.12, K.14, R.15, P.21, F.22, V.23, K.26, I.27, A.30, V.71, V.74, Q.75, Y.94 Ligands: DTP.8, MG.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.27 Hydrogen bonds: B:P.21, B:V.23, B:Q.75 Salt bridges: B:K.14, B:K.14, B:K.14, B:R.15, B:K.26, B:K.26, B:K.26 DTP.8: 14 residues within 4Å: Chain B: R.15, A.30, N.33, A.34, A.37, Q.75, A.93, Y.94, Y.97, R.98, R.101, R.105 Ligands: DTP.7, MG.9 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.94, B:Y.97 Hydrogen bonds: B:Q.75 Water bridges: B:Y.97, B:Y.97 Salt bridges: B:R.15, B:R.15, B:R.101, B:R.101, B:R.101, B:R.105 pi-Stacking: B:Y.97, B:Y.97 DTP.13: 15 residues within 4Å: Chain C: I.12, K.14, R.15, P.21, F.22, V.23, K.26, I.27, A.30, V.71, V.74, Q.75, Y.94 Ligands: DTP.14, MG.15 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.27 Hydrogen bonds: C:P.21, C:V.23, C:Q.75, C:Y.94 Water bridges: C:R.15, C:R.15, C:A.30 Salt bridges: C:K.14, C:K.14, C:K.14, C:R.15, C:K.26, C:K.26, C:K.26 DTP.14: 14 residues within 4Å: Chain C: R.15, A.30, N.33, A.34, A.37, Q.75, A.93, Y.94, Y.97, R.98, R.101, R.105 Ligands: DTP.13, MG.15 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.94, C:Y.97 Hydrogen bonds: C:Q.75, C:Y.97 Water bridges: C:R.105, C:R.105 Salt bridges: C:R.15, C:R.15, C:R.105, C:R.105 pi-Stacking: C:Y.97, C:Y.97 DTP.19: 15 residues within 4Å: Chain D: I.12, K.14, R.15, P.21, F.22, V.23, K.26, I.27, A.30, V.71, V.74, Q.75, Y.94 Ligands: DTP.20, MG.21 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.27 Hydrogen bonds: D:P.21, D:V.23, D:Q.75 Salt bridges: D:K.14, D:K.14, D:K.14, D:R.15, D:K.26, D:K.26, D:K.26 DTP.20: 14 residues within 4Å: Chain D: R.15, A.30, N.33, A.34, A.37, Q.75, A.93, Y.94, Y.97, R.98, R.101, R.105 Ligands: DTP.19, MG.21 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Y.94, D:Y.97 Hydrogen bonds: D:Q.75 Water bridges: D:R.15, D:R.15 Salt bridges: D:R.15, D:R.15, D:R.101, D:R.101, D:R.101, D:R.105, D:R.105 pi-Stacking: D:Y.97, D:Y.97

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 2 residues within 4Å: Ligands: DTP.1, DTP.2 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Ligands: DTP.7, DTP.8 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Ligands: DTP.13, DTP.14 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Ligands: DTP.19, DTP.20 No protein-ligand interaction detected (PLIP)

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

MN.4: 5 residues within 4Å: Chain A: E.203, E.266, E.301, H.304 Ligands: MN.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.266, A:E.301, A:H.304, H2O.1, H2O.1 MN.5: 5 residues within 4Å: Chain A: E.173, E.203, H.206, E.301 Ligands: MN.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.173, A:E.203, A:E.203, A:H.206, A:E.301 MN.10: 5 residues within 4Å: Chain B: E.173, E.203, H.206, E.301 Ligands: MN.11 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.173, B:E.203, B:E.203, B:H.206, B:E.301 MN.11: 5 residues within 4Å: Chain B: E.203, E.266, E.301, H.304 Ligands: MN.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.203, B:E.266, B:E.301, B:H.304, H2O.2 MN.16: 5 residues within 4Å: Chain C: E.173, E.203, H.206, E.301 Ligands: MN.17 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.173, C:E.203, C:H.206, C:E.301, H2O.4 MN.17: 5 residues within 4Å: Chain C: E.203, E.266, E.301, H.304 Ligands: MN.16 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.266, C:E.301, C:E.301, C:H.304, H2O.4 MN.22: 5 residues within 4Å: Chain D: E.173, E.203, H.206, E.301 Ligands: MN.23 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.173, D:E.203, D:E.203, D:H.206, D:E.301 MN.23: 5 residues within 4Å: Chain D: E.203, E.266, E.301, H.304 Ligands: MN.22 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.266, D:E.301, D:E.301, D:H.304, H2O.5

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 7 residues within 4Å: Chain A: F.110, E.111, K.112, H.185, R.186, P.188, D.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.110 TRS.12: 6 residues within 4Å: Chain B: F.110, E.111, K.112, R.186, P.188, D.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.110, B:R.186, B:D.251 TRS.18: 7 residues within 4Å: Chain C: F.110, E.111, H.185, R.186, P.188, D.249, D.251 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.110, C:R.186, C:R.186 TRS.24: 8 residues within 4Å: Chain D: F.110, E.111, K.112, H.185, R.186, P.188, D.249, D.251 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.249, D:D.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rozman Grinberg, I. et al., Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit. Elife (2018)

Release Date

2018-01-10

Peptides

Ribonucleoside-diphosphate reductase, beta subunit 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ribonucleoside-diphosphate reductase, beta subunit 1