SMTL ID : 6mw3.1 (1 other biounit)

EM structure of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha subunit and NrdF beta subunit with dATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Ribonucleoside-diphosphate reductase NrdF beta subunit(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 3 residues within 4Å: Chain A: R.293, T.664, L.672 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.672 Hydrogen bonds: A:T.664, A:T.664 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.2: 4 residues within 4Å: Chain B: M.662, T.663, T.664, R.665 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.663 Hydrogen bonds: B:M.662, B:T.664, B:T.664, B:R.665 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.7: 3 residues within 4Å: Chain C: R.293, T.664, L.672 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.672 Hydrogen bonds: C:T.664, C:T.664 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.8: 4 residues within 4Å: Chain D: M.662, T.663, T.664, R.665 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:T.663 Hydrogen bonds: D:M.662, D:T.664, D:T.664, D:R.665 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.13: 3 residues within 4Å: Chain E: R.293, T.664, L.672 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.672 Hydrogen bonds: E:T.664, E:T.664 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.14: 4 residues within 4Å: Chain F: M.662, T.663, T.664, R.665 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:T.663 Hydrogen bonds: F:M.662, F:T.664, F:T.664, F:R.665 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.19: 3 residues within 4Å: Chain G: R.293, T.664, L.672 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:L.672 Hydrogen bonds: G:T.664, G:T.664 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.20: 4 residues within 4Å: Chain H: M.662, T.663, T.664, R.665 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:T.663 Hydrogen bonds: H:M.662, H:T.664, H:T.664, H:R.665 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.25: 3 residues within 4Å: Chain I: R.293, T.664, L.672 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:L.672 Hydrogen bonds: I:T.664, I:T.664 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.26: 4 residues within 4Å: Chain J: M.662, T.663, T.664, R.665 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:T.663 Hydrogen bonds: J:M.662, J:T.664, J:T.664, J:R.665 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.31: 3 residues within 4Å: Chain K: R.293, T.664, L.672 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:L.672 Hydrogen bonds: K:T.664, K:T.664 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.32: 4 residues within 4Å: Chain L: M.662, T.663, T.664, R.665 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:T.663 Hydrogen bonds: L:M.662, L:T.664, L:T.664, L:R.665

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

DTP.3: 9 residues within 4Å: Chain A: D.177, S.178, L.179, R.207, I.213, K.214 Chain B: K.194, Y.236, A.237 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:Y.236, A:D.177, A:D.177, A:L.179 Salt bridges: B:K.194, A:R.207, A:K.214, A:K.214, A:K.214, A:H.304 DTP.4: 8 residues within 4Å: Chain A: V.33, H.34, F.37, N.42, F.89, R.90, F.91 Chain D: H.49 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.42, A:F.91, A:F.91, D:E.53 Salt bridges: A:H.34, A:K.88, A:R.90, A:R.90 pi-Stacking: A:F.37, A:F.37 pi-Cation interactions: A:R.90 DTP.5: 10 residues within 4Å: Chain A: K.194, Y.236, A.237 Chain B: D.177, S.178, L.179, R.207, I.213, K.214, H.304 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Y.236, B:D.177, B:L.179 Salt bridges: A:K.194, B:R.207, B:K.214, B:K.214, B:K.214, B:H.304 DTP.6: 7 residues within 4Å: Chain B: V.33, H.34, F.37, N.42, F.89, R.90, F.91 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.42, B:F.91, B:F.91 Salt bridges: B:H.34, B:K.88, B:R.90, B:R.90 pi-Stacking: B:F.37, B:F.37 pi-Cation interactions: B:R.90 DTP.9: 9 residues within 4Å: Chain C: D.177, S.178, L.179, R.207, I.213, K.214 Chain D: K.194, Y.236, A.237 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.177, C:D.177, C:L.179 Salt bridges: C:R.207, C:K.214, C:K.214, C:K.214, C:H.304, D:K.194 DTP.10: 8 residues within 4Å: Chain C: V.33, H.34, F.37, N.42, F.89, R.90, F.91 Chain F: H.49 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:N.42, C:F.91, C:F.91, F:E.53 Salt bridges: C:H.34, C:K.88, C:R.90, C:R.90 pi-Stacking: C:F.37, C:F.37 pi-Cation interactions: C:R.90 DTP.11: 10 residues within 4Å: Chain C: K.194, Y.236, A.237 Chain D: D.177, S.178, L.179, R.207, I.213, K.214, H.304 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.177, D:L.179 Salt bridges: D:R.207, D:K.214, D:K.214, D:K.214, D:H.304, C:K.194 DTP.12: 9 residues within 4Å: Chain A: H.49, E.53 Chain D: V.33, H.34, F.37, N.42, F.89, R.90, F.91 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.42, D:F.91, D:F.91, A:E.53 Salt bridges: D:H.34, D:K.88, D:R.90, D:R.90 pi-Stacking: D:F.37, D:F.37 pi-Cation interactions: D:R.90 DTP.15: 9 residues within 4Å: Chain E: D.177, S.178, L.179, R.207, I.213, K.214 Chain F: K.194, Y.236, A.237 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:D.177, E:D.177, E:L.179 Salt bridges: E:R.207, E:K.214, E:K.214, E:K.214, E:H.304, F:K.194 DTP.16: 8 residues within 4Å: Chain E: V.33, H.34, F.37, N.42, F.89, R.90, F.91 Chain H: H.49 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:N.42, E:F.91, E:F.91, H:E.53 Salt bridges: E:H.34, E:K.88, E:R.90, E:R.90 pi-Stacking: E:F.37, E:F.37 pi-Cation interactions: E:R.90 DTP.17: 10 residues within 4Å: Chain E: K.194, Y.236, A.237 Chain F: D.177, S.178, L.179, R.207, I.213, K.214, H.304 9 PLIP interactions: 2 interactions with chain E, 7 interactions with chain F Hydrogen bonds: E:Y.236, F:D.177, F:L.179 Salt bridges: E:K.194, F:R.207, F:K.214, F:K.214, F:K.214, F:H.304 DTP.18: 9 residues within 4Å: Chain C: H.49, E.53 Chain F: V.33, H.34, F.37, N.42, F.89, R.90, F.91 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:N.42, F:F.91, F:F.91, C:E.53 Salt bridges: F:H.34, F:K.88, F:R.90, F:R.90 pi-Stacking: F:F.37, F:F.37 pi-Cation interactions: F:R.90 DTP.21: 9 residues within 4Å: Chain G: D.177, S.178, L.179, R.207, I.213, K.214 Chain H: K.194, Y.236, A.237 9 PLIP interactions: 8 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:D.177, G:D.177, G:L.179 Salt bridges: G:R.207, G:K.214, G:K.214, G:K.214, G:H.304, H:K.194 DTP.22: 8 residues within 4Å: Chain G: V.33, H.34, F.37, N.42, F.89, R.90, F.91 Chain J: H.49 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain J Hydrogen bonds: G:N.42, G:F.91, G:F.91, J:E.53 Salt bridges: G:H.34, G:K.88, G:R.90, G:R.90 pi-Stacking: G:F.37, G:F.37 pi-Cation interactions: G:R.90 DTP.23: 10 residues within 4Å: Chain G: K.194, Y.236, A.237 Chain H: D.177, S.178, L.179, R.207, I.213, K.214, H.304 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:D.177, H:L.179, G:Y.236 Salt bridges: H:R.207, H:K.214, H:K.214, H:K.214, H:H.304, G:K.194 DTP.24: 9 residues within 4Å: Chain E: H.49, E.53 Chain H: V.33, H.34, F.37, N.42, F.89, R.90, F.91 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:N.42, H:F.91, H:F.91, E:E.53 Salt bridges: H:H.34, H:K.88, H:R.90, H:R.90 pi-Stacking: H:F.37, H:F.37 pi-Cation interactions: H:R.90 DTP.27: 9 residues within 4Å: Chain I: D.177, S.178, L.179, R.207, I.213, K.214 Chain J: K.194, Y.236, A.237 10 PLIP interactions: 2 interactions with chain J, 8 interactions with chain I Hydrogen bonds: J:Y.236, I:D.177, I:D.177, I:L.179 Salt bridges: J:K.194, I:R.207, I:K.214, I:K.214, I:K.214, I:H.304 DTP.28: 8 residues within 4Å: Chain I: V.33, H.34, F.37, N.42, F.89, R.90, F.91 Chain L: H.49 11 PLIP interactions: 10 interactions with chain I, 1 interactions with chain L Hydrogen bonds: I:N.42, I:F.91, I:F.91, L:E.53 Salt bridges: I:H.34, I:K.88, I:R.90, I:R.90 pi-Stacking: I:F.37, I:F.37 pi-Cation interactions: I:R.90 DTP.29: 10 residues within 4Å: Chain I: K.194, Y.236, A.237 Chain J: D.177, S.178, L.179, R.207, I.213, K.214, H.304 9 PLIP interactions: 7 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:D.177, J:L.179, I:Y.236 Salt bridges: J:R.207, J:K.214, J:K.214, J:K.214, J:H.304, I:K.194 DTP.30: 9 residues within 4Å: Chain G: H.49, E.53 Chain J: V.33, H.34, F.37, N.42, F.89, R.90, F.91 11 PLIP interactions: 1 interactions with chain G, 10 interactions with chain J Hydrogen bonds: G:E.53, J:N.42, J:F.91, J:F.91 Salt bridges: J:H.34, J:K.88, J:R.90, J:R.90 pi-Stacking: J:F.37, J:F.37 pi-Cation interactions: J:R.90 DTP.33: 9 residues within 4Å: Chain K: D.177, S.178, L.179, R.207, I.213, K.214 Chain L: K.194, Y.236, A.237 9 PLIP interactions: 8 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:D.177, K:D.177, K:L.179 Salt bridges: K:R.207, K:K.214, K:K.214, K:K.214, K:H.304, L:K.194 DTP.34: 7 residues within 4Å: Chain K: V.33, H.34, F.37, N.42, F.89, R.90, F.91 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:N.42, K:F.91, K:F.91 Salt bridges: K:H.34, K:K.88, K:R.90, K:R.90 pi-Stacking: K:F.37, K:F.37 pi-Cation interactions: K:R.90 DTP.35: 10 residues within 4Å: Chain K: K.194, Y.236, A.237 Chain L: D.177, S.178, L.179, R.207, I.213, K.214, H.304 8 PLIP interactions: 7 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:D.177, L:L.179 Salt bridges: L:R.207, L:K.214, L:K.214, L:K.214, L:H.304, K:K.194 DTP.36: 9 residues within 4Å: Chain I: H.49, E.53 Chain L: V.33, H.34, F.37, N.42, F.89, R.90, F.91 11 PLIP interactions: 10 interactions with chain L, 1 interactions with chain I Hydrogen bonds: L:N.42, L:F.91, L:F.91, I:E.53 Salt bridges: L:H.34, L:K.88, L:R.90, L:R.90 pi-Stacking: L:F.37, L:F.37 pi-Cation interactions: L:R.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, W.C. et al., Convergent allostery in ribonucleotide reductase. Nat Commun (2019)

Release Date

2019-06-19

Peptides

Ribonucleoside-diphosphate reductase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

E
C

F
D

G
C

H
D

I
C

J
D

K
C

L
D

Ribonucleoside-diphosphate reductase

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