SMTL ID : 7p37.1

Streptomyces coelicolor ATP-loaded NrdR

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

ATP.1: 14 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, Y.128 Ligands: ATP.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.51, A:P.57, A:S.59, A:Y.128, A:Y.128 Salt bridges: A:K.50, A:K.50, A:R.51, A:R.51 ATP.2: 9 residues within 4Å: Chain A: K.50, E.56, K.62, K.69, A.70, F.124, Y.128 Ligands: ATP.1, ATP.19 6 PLIP interactions: 1 interactions with chain G, 5 interactions with chain A Hydrogen bonds: G:Q.72, A:Y.128, A:Y.128 Salt bridges: A:K.50, A:K.50, A:K.62 ATP.4: 14 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, Y.128 Ligands: ATP.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.51, B:P.57, B:S.59, B:Y.128, B:Y.128 Salt bridges: B:K.50, B:K.50, B:R.51, B:R.51 ATP.5: 9 residues within 4Å: Chain B: K.50, E.56, K.62, K.69, A.70, F.124, Y.128 Ligands: ATP.4, ATP.22 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:Y.128, B:Y.128, H:Q.72 Salt bridges: B:K.50, B:K.50, B:K.62 ATP.7: 14 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, Y.128 Ligands: ATP.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.51, C:P.57, C:S.59, C:Y.128, C:Y.128 Salt bridges: C:K.50, C:K.50, C:R.51, C:R.51 ATP.8: 9 residues within 4Å: Chain C: K.50, E.56, K.62, K.69, A.70, F.124, Y.128 Ligands: ATP.7, ATP.25 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain I Hydrogen bonds: C:Y.128, C:Y.128, I:Q.72 Salt bridges: C:K.50, C:K.50, C:K.62 ATP.10: 14 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, Y.128 Ligands: ATP.11 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:R.51, D:E.56, D:P.57, D:S.59, D:T.102, D:Y.128, D:Y.128 Salt bridges: D:K.50, D:K.50, D:R.51, D:R.51 ATP.11: 9 residues within 4Å: Chain D: K.50, E.56, K.62, K.69, A.70, F.124, Y.128 Ligands: ATP.10, ATP.28 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain J Hydrogen bonds: D:Y.128, J:Q.72 Salt bridges: D:K.50, D:K.50, D:K.62 ATP.13: 14 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, Y.128 Ligands: ATP.14 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:R.51, E:E.56, E:P.57, E:S.59, E:T.102, E:Y.128, E:Y.128 Salt bridges: E:K.50, E:K.50, E:R.51, E:R.51 ATP.14: 9 residues within 4Å: Chain E: K.50, E.56, K.62, K.69, A.70, F.124, Y.128 Ligands: ATP.13, ATP.31 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain K Hydrogen bonds: E:Y.128, K:Q.72 Salt bridges: E:K.50, E:K.50, E:K.62 ATP.16: 14 residues within 4Å: 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, Y.128 Ligands: ATP.17 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:R.51, F:E.56, F:P.57, F:S.59, F:T.102, F:Y.128, F:Y.128 Salt bridges: F:K.50, F:K.50, F:R.51, F:R.51 ATP.17: 9 residues within 4Å: Chain F: K.50, E.56, K.62, K.69, A.70, F.124, Y.128 Ligands: ATP.16, ATP.34 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.128 Salt bridges: F:K.50, F:K.50, F:K.62 ATP.19: 11 residues within 4Å: Chain A: K.69 Chain G: K.50, K.62, G.66, K.69, A.70, Q.72, F.124, Y.128 Ligands: ATP.2, ATP.20 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:Y.128 Salt bridges: G:K.50, G:K.50, G:K.62, G:K.62, G:K.69, A:K.69 ATP.20: 17 residues within 4Å: Chain A: K.69, Q.72 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: ATP.19 15 PLIP interactions: 5 interactions with chain A, 9 interactions with chain G, 1 interactions with chain B Hydrogen bonds: A:Q.72, A:Q.72, G:K.50, G:R.51, G:P.57, G:S.59, G:T.102, G:Y.128, B:R.17 Salt bridges: A:K.69, A:K.69, A:K.69, G:K.50, G:K.50, G:R.51 ATP.22: 11 residues within 4Å: Chain B: K.69 Chain H: K.50, K.62, G.66, K.69, A.70, Q.72, F.124, Y.128 Ligands: ATP.5, ATP.23 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:Y.128 Salt bridges: H:K.50, H:K.50, H:K.62, H:K.62, H:K.69, B:K.69 ATP.23: 18 residues within 4Å: Chain B: K.69, Q.72 Chain C: R.17 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: ATP.22 15 PLIP interactions: 9 interactions with chain H, 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: H:K.50, H:R.51, H:P.57, H:S.59, H:T.102, H:Y.128, B:Q.72, B:Q.72, C:R.17 Salt bridges: H:K.50, H:K.50, H:R.51, B:K.69, B:K.69, B:K.69 ATP.25: 11 residues within 4Å: Chain C: K.69 Chain I: K.50, K.62, G.66, K.69, A.70, Q.72, F.124, Y.128 Ligands: ATP.8, ATP.26 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain I Salt bridges: C:K.69, I:K.50, I:K.50, I:K.62, I:K.62, I:K.69 Hydrogen bonds: I:Y.128 ATP.26: 17 residues within 4Å: Chain C: K.69, Q.72 Chain I: 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: ATP.25 15 PLIP interactions: 5 interactions with chain C, 9 interactions with chain I, 1 interactions with chain A Hydrogen bonds: C:Q.72, C:Q.72, I:K.50, I:R.51, I:P.57, I:S.59, I:T.102, I:Y.128, A:R.17 Salt bridges: C:K.69, C:K.69, C:K.69, I:K.50, I:K.50, I:R.51 ATP.28: 11 residues within 4Å: Chain D: K.69 Chain J: K.50, K.62, G.66, K.69, A.70, Q.72, F.124, Y.128 Ligands: ATP.11, ATP.29 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain D Salt bridges: J:K.50, J:K.50, J:K.62, J:K.62, J:K.69, D:K.69 ATP.29: 18 residues within 4Å: Chain D: K.69, Q.72 Chain F: R.17 Chain J: 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: ATP.28 16 PLIP interactions: 5 interactions with chain D, 1 interactions with chain F, 10 interactions with chain J Hydrogen bonds: D:Q.72, D:Q.72, F:R.17, J:K.50, J:R.51, J:P.57, J:S.59, J:T.102, J:Y.128, J:Y.128 Salt bridges: D:K.69, D:K.69, D:K.69, J:K.50, J:K.50, J:R.51 ATP.31: 11 residues within 4Å: Chain E: K.69 Chain K: K.50, K.62, G.66, K.69, A.70, Q.72, F.124, Y.128 Ligands: ATP.14, ATP.32 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain K Salt bridges: E:K.69, K:K.50, K:K.50, K:K.62, K:K.62, K:K.69 ATP.32: 17 residues within 4Å: Chain E: K.69, Q.72 Chain K: 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: ATP.31 16 PLIP interactions: 10 interactions with chain K, 5 interactions with chain E, 1 interactions with chain D Hydrogen bonds: K:K.50, K:R.51, K:P.57, K:S.59, K:T.102, K:Y.128, K:Y.128, E:Q.72, E:Q.72, D:R.17 Salt bridges: K:K.50, K:K.50, K:R.51, E:K.69, E:K.69, E:K.69 ATP.34: 11 residues within 4Å: Chain F: K.69 Chain L: K.50, K.62, G.66, K.69, A.70, Q.72, F.124, Y.128 Ligands: ATP.17, ATP.35 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain F Salt bridges: L:K.50, L:K.50, L:K.62, L:K.62, L:K.69, F:K.69 ATP.35: 17 residues within 4Å: Chain F: K.69, Q.72 Chain L: 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: ATP.34 16 PLIP interactions: 5 interactions with chain F, 10 interactions with chain L, 1 interactions with chain E Hydrogen bonds: F:Q.72, F:Q.72, L:K.50, L:R.51, L:P.57, L:S.59, L:T.102, L:Y.128, L:Y.128, E:R.17 Salt bridges: F:K.69, F:K.69, F:K.69, L:K.50, L:K.50, L:R.51

12 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: 4 residues within 4Å: Chain E: C.3, 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: 4 residues within 4Å: Chain F: C.3, 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: 4 residues within 4Å: Chain G: C.3, 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: 4 residues within 4Å: Chain H: C.3, 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 ZN.27: 4 residues within 4Å: Chain I: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.3, I:C.6, I:C.31, I:C.34 ZN.30: 4 residues within 4Å: Chain J: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.3, J:C.6, J:C.31, J:C.34 ZN.33: 4 residues within 4Å: Chain K: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.3, K:C.6, K:C.31, K:C.34 ZN.36: 4 residues within 4Å: Chain L: C.3, C.6, C.31, C.34 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.3, L:C.6, L:C.31, L: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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
I

D
C

E
G

F
K

G
B

H
F

I
J

J
D

K
H

L
L

Transcriptional repressor NrdR

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