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

EM structure of Bacillus subtilis ribonucleotide reductase inhibited double-helical filament of NrdE alpha subunit with dATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

DTP.1: 10 residues within 4Å: Chain A: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 Chain B: K.194, Y.236 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain A Salt bridges: B:K.194, A:R.207, A:K.214, A:K.214, A:K.214, A:H.304 Hydrophobic interactions: A:L.179, A:I.182 Hydrogen bonds: A:D.177, A:L.179 DTP.2: 11 residues within 4Å: Chain A: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 Chain F: H.49, E.53 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.42, A:R.90, A:F.91, A:F.91 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.3: 10 residues within 4Å: Chain A: K.194, Y.236 Chain B: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.179, B:I.182 Hydrogen bonds: B:D.177, B:D.177, B:L.179 Salt bridges: B:R.207, B:K.214, B:K.214, B:K.214, B:H.304, A:K.194 DTP.4: 11 residues within 4Å: Chain B: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 Chain I: H.49, E.53 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.42, B:R.90, 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.5: 10 residues within 4Å: Chain C: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 Chain D: K.194, Y.236 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain C Salt bridges: D:K.194, C:R.207, C:K.214, C:K.214, C:K.214, C:H.304 Hydrophobic interactions: C:L.179, C:I.182 Hydrogen bonds: C:D.177, C:L.179 DTP.6: 11 residues within 4Å: Chain C: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 Chain H: H.49, E.53 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.42, C:R.90, C:F.91, C:F.91 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.7: 10 residues within 4Å: Chain C: K.194, Y.236 Chain D: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.179, D:I.182 Hydrogen bonds: D:D.177, 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.8: 12 residues within 4Å: Chain D: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 Chain K: H.49, E.53, D.56 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain K Hydrogen bonds: D:N.42, D:R.90, D:F.91, D:F.91, K:D.56 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.9: 10 residues within 4Å: Chain E: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 Chain F: K.194, Y.236 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:L.179, E:I.182 Hydrogen bonds: 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.10: 9 residues within 4Å: Chain E: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:N.42, E:R.90, E:F.91, E:F.91 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.11: 10 residues within 4Å: Chain E: K.194, Y.236 Chain F: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:L.179, F:I.182 Hydrogen bonds: F:D.177, F:D.177, F:L.179 Salt bridges: F:R.207, F:K.214, F:K.214, F:K.214, F:H.304, E:K.194 DTP.12: 11 residues within 4Å: Chain A: H.49, E.53 Chain F: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:N.42, F:R.90, F:F.91, F:F.91 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.13: 10 residues within 4Å: Chain G: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 Chain H: K.194, Y.236 10 PLIP interactions: 9 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:L.179, G:I.182 Hydrogen bonds: 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.14: 9 residues within 4Å: Chain G: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:N.42, G:R.90, G:F.91, G:F.91 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.15: 10 residues within 4Å: Chain G: K.194, Y.236 Chain H: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:L.179, H:I.182 Hydrogen bonds: H:D.177, H:D.177, H:L.179 Salt bridges: H:R.207, H:K.214, H:K.214, H:K.214, H:H.304, G:K.194 DTP.16: 11 residues within 4Å: Chain C: H.49, E.53 Chain H: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:N.42, H:R.90, H:F.91, H:F.91 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.17: 10 residues within 4Å: Chain I: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 Chain J: K.194, Y.236 10 PLIP interactions: 9 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:L.179, I:I.182 Hydrogen bonds: I:D.177, I:L.179 Salt bridges: I:R.207, I:K.214, I:K.214, I:K.214, I:H.304, J:K.194 DTP.18: 11 residues within 4Å: Chain B: H.49, E.53 Chain I: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:N.42, I:R.90, I:F.91, I:F.91 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.19: 10 residues within 4Å: Chain I: K.194, Y.236 Chain J: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 11 PLIP interactions: 10 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:L.179, J:I.182 Hydrogen bonds: J:D.177, J:D.177, J:L.179 Salt bridges: J:R.207, J:K.214, J:K.214, J:K.214, J:H.304, I:K.194 DTP.20: 9 residues within 4Å: Chain J: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:N.42, J:R.90, 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.21: 10 residues within 4Å: Chain K: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 Chain L: K.194, Y.236 10 PLIP interactions: 9 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:L.179, K:I.182 Hydrogen bonds: 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.22: 12 residues within 4Å: Chain D: H.49, E.53, D.56 Chain K: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 13 PLIP interactions: 11 interactions with chain K, 2 interactions with chain D Hydrogen bonds: K:N.42, K:R.90, K:F.91, K:F.91, D:D.56, D:D.56 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.23: 10 residues within 4Å: Chain K: K.194, Y.236 Chain L: D.177, S.178, L.179, I.182, R.207, I.213, K.214, H.304 11 PLIP interactions: 1 interactions with chain K, 10 interactions with chain L Salt bridges: K:K.194, L:R.207, L:K.214, L:K.214, L:K.214, L:H.304 Hydrophobic interactions: L:L.179, L:I.182 Hydrogen bonds: L:D.177, L:D.177, L:L.179 DTP.24: 9 residues within 4Å: Chain L: V.33, H.34, F.37, V.38, N.42, K.88, F.89, R.90, F.91 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:N.42, L:R.90, L:F.91, L:F.91 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
I

D
J

E
C

F
D

G
I

H
J

I
C

J
D

K
I

L
J

Ribonucleoside-diphosphate reductase

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