SMTL ID : 7p3q.1

Streptomyces coelicolor dATP/ATP-loaded NrdR octamer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 15 residues within 4Å: Chain A: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.51, A:E.56, A:P.57, A:S.59, A:K.62, A:T.102 Salt bridges: A:K.50, A:R.51 ATP.4: 15 residues within 4Å: Chain B: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.51, B:P.57, B:S.59, B:K.62, B:T.102 Salt bridges: B:K.50, B:R.51 ATP.7: 15 residues within 4Å: Chain C: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.51, C:E.56, C:P.57, C:S.59, C:K.62, C:T.102 Salt bridges: C:K.50, C:R.51 ATP.10: 15 residues within 4Å: Chain D: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.11 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.51, D:P.57, D:S.59, D:K.62, D:T.102 Salt bridges: D:K.50, D:R.51 ATP.13: 15 residues within 4Å: Chain E: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.14 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:K.50, E:R.51, E:P.57, E:S.59, E:K.62, E:T.102, C:R.26 Salt bridges: E:K.50, E:K.50, E:R.51, E:R.51 ATP.16: 16 residues within 4Å: Chain D: R.26 Chain F: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.17 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:K.50, F:R.51, F:E.56, F:P.57, F:S.59, F:K.62 Salt bridges: F:K.50, F:K.50, F:R.51, F:R.51, D:R.26 ATP.19: 16 residues within 4Å: Chain A: R.26 Chain G: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.20 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain A Hydrogen bonds: G:K.50, G:R.51, G:P.57, G:S.59, G:K.62, G:T.102, A:R.26, A:R.26 Salt bridges: G:K.50, G:K.50, G:R.51, G:R.51 ATP.22: 15 residues within 4Å: Chain H: V.48, K.50, R.51, E.56, P.57, F.58, S.59, K.62, V.63, T.102, V.105, I.109, F.124, Y.128 Ligands: DTP.23 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:K.50, H:R.51, H:E.56, H:P.57, H:S.59, H:K.62, B:R.26 Salt bridges: H:K.50, H:K.50, H:R.51, H:R.51

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

DTP.2: 14 residues within 4Å: Chain A: K.50, E.56, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Chain E: K.69, Q.72 Ligands: ATP.1, DTP.14 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:F.124, A:V.127 Hydrogen bonds: A:E.56, E:K.69, E:Q.72 Salt bridges: A:K.50, A:K.62, A:K.62, A:K.69 DTP.5: 14 residues within 4Å: Chain B: K.50, E.56, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Chain F: K.69, Q.72 Ligands: ATP.4, DTP.17 9 PLIP interactions: 2 interactions with chain F, 7 interactions with chain B Hydrogen bonds: F:K.69, F:Q.72, B:E.56 Hydrophobic interactions: B:F.124, B:V.127 Salt bridges: B:K.50, B:K.62, B:K.62, B:K.69 DTP.8: 14 residues within 4Å: Chain C: K.50, E.56, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Chain G: K.69, Q.72 Ligands: ATP.7, DTP.20 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:F.124, C:V.127 Hydrogen bonds: C:E.56, G:K.69, G:Q.72 Salt bridges: C:K.50, C:K.62, C:K.62, C:K.69 DTP.11: 14 residues within 4Å: Chain D: K.50, E.56, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Chain H: K.69, Q.72 Ligands: ATP.10, DTP.23 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain H Hydrophobic interactions: D:F.124, D:V.127 Hydrogen bonds: D:E.56, H:K.69, H:Q.72 Salt bridges: D:K.50, D:K.62, D:K.62, D:K.69 DTP.14: 13 residues within 4Å: Chain A: K.69, Q.72 Chain E: K.50, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Ligands: DTP.2, ATP.13 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:F.124, E:V.127 Salt bridges: E:K.50, E:K.50, E:K.62, E:K.62, E:K.69 Hydrogen bonds: A:Q.72, A:Q.72 DTP.17: 13 residues within 4Å: Chain B: K.69, Q.72 Chain F: K.50, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Ligands: DTP.5, ATP.16 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:F.124, F:V.127 Salt bridges: F:K.50, F:K.50, F:K.62, F:K.62, F:K.69 Hydrogen bonds: B:Q.72 DTP.20: 13 residues within 4Å: Chain C: K.69, Q.72 Chain G: K.50, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Ligands: DTP.8, ATP.19 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:F.124, G:V.127 Salt bridges: G:K.50, G:K.50, G:K.62, G:K.62, G:K.69 Hydrogen bonds: C:Q.72 DTP.23: 13 residues within 4Å: Chain D: K.69, Q.72 Chain H: K.50, K.62, G.66, K.69, A.70, R.123, F.124, V.127, Y.128 Ligands: DTP.11, ATP.22 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:F.124, H:V.127 Salt bridges: H:K.50, H:K.50, H:K.62, H:K.62, H:K.69 Hydrogen bonds: D:Q.72, D:Q.72

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.3, A:C.6, A:C.31, A:C.34 ZN.6: 4 residues within 4Å: Chain B: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.3, B:C.6, B:C.31, B:C.34 ZN.9: 4 residues within 4Å: Chain C: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.3, C:C.6, C:C.31, C:C.34 ZN.12: 4 residues within 4Å: Chain D: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.3, D:C.6, D:C.31, D:C.34 ZN.15: 5 residues within 4Å: Chain E: C.3, F.5, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.3, E:C.6, E:C.31, E:C.34 ZN.18: 5 residues within 4Å: Chain F: C.3, F.5, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.3, F:C.6, F:C.31, F:C.34 ZN.21: 5 residues within 4Å: Chain G: C.3, F.5, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.3, G:C.6, G:C.31, G:C.34 ZN.24: 5 residues within 4Å: Chain H: C.3, F.5, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.3, H:C.6, H:C.31, H:C.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rozman Grinberg, I. et al., A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases. Nat Commun (2022)

Release Date

2022-05-11

Peptides

Transcriptional repressor NrdR: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

E
B

F
D

G
F

H
H

Transcriptional repressor NrdR

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