SMTL ID : 9kbi.1

The structure of B19V NS1_2-570/dsDNA/AMPPNP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Covalent)(Non-covalent)

ANP.1: 14 residues within 4Å: Chain A: P.328, P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, C.447, S.448, M.451, L.453 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.330, A:T.331, A:G.332, A:K.333, A:K.333, A:T.334, A:N.335, A:N.414 ANP.3: 15 residues within 4Å: Chain B: P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, C.447, S.448, P.449, D.450, M.451, G.452, L.453 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.330, B:T.331, B:G.332, B:K.333, B:K.333, B:K.333, B:T.334, B:T.334, B:T.334, B:N.335, B:N.335, B:N.414, B:S.448, B:M.451, B:G.452 ANP.4: 13 residues within 4Å: Chain C: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, P.449, M.451, G.452, L.453 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.330, C:S.330, C:T.331, C:G.332, C:K.333, C:K.333, C:K.333, C:K.333, C:T.334, C:T.334, C:N.335, C:N.335, C:N.414, C:G.452 ANP.5: 16 residues within 4Å: Chain D: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, C.447, S.448, P.449, M.451, G.452, L.453 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.330, D:S.330, D:T.331, D:G.332, D:K.333, D:K.333, D:K.333, D:T.334, D:N.335, D:N.335, D:N.414, D:S.448, D:M.451 ANP.7: 11 residues within 4Å: Chain E: P.328, P.329, S.330, T.331, G.332, K.333, T.334, N.335, M.451, G.452, L.453 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.330, E:T.331, E:G.332, E:K.333, E:K.333, E:K.333, E:T.334, E:T.334, E:N.335, E:N.335, E:C.447 ANP.8: 15 residues within 4Å: Chain F: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, S.448, P.449, M.451, G.452, L.453 Ligands: MG.9 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:S.330, F:T.331, F:G.332, F:K.333, F:K.333, F:T.334, F:N.335, F:N.335, F:N.414, F:M.451 ANP.10: 16 residues within 4Å: Chain G: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, C.447, S.448, P.449, D.450, M.451, G.452, L.453 Ligands: MG.11 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:S.330, G:T.331, G:G.332, G:K.333, G:K.333, G:T.334, G:T.334, G:N.335, G:E.372, G:L.453 ANP.12: 17 residues within 4Å: Chain H: P.328, P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, C.447, S.448, P.449, D.450, M.451, G.452, L.453 Ligands: MG.13 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:S.330, H:T.331, H:G.332, H:K.333, H:K.333, H:K.333, H:T.334, H:T.334, H:N.335, H:N.335, H:N.414, H:S.448, H:M.451, H:G.452 ANP.14: 14 residues within 4Å: Chain I: P.328, P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, S.448, P.449, G.452, L.453 Ligands: MG.15 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:S.330, I:S.330, I:T.331, I:G.332, I:K.333, I:K.333, I:K.333, I:T.334, I:T.334, I:N.335, I:N.335, I:N.414 ANP.16: 15 residues within 4Å: Chain J: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, C.447, S.448, P.449, D.450, L.453 Ligands: MG.17 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:S.330, J:T.331, J:G.332, J:K.333, J:K.333, J:K.333, J:K.333, J:T.334, J:T.334, J:N.335, J:E.372, J:N.414 ANP.18: 13 residues within 4Å: Chain K: P.328, P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, C.447, M.451, L.453 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:S.330, K:T.331, K:G.332, K:K.333, K:K.333, K:K.333, K:T.334, K:T.334, K:N.335, K:N.335, K:E.372, K:N.414, K:N.414 ANP.19: 16 residues within 4Å: Chain L: P.328, P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, C.447, S.448, P.449, G.452, L.453 Ligands: MG.20 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:S.330, L:T.331, L:G.332, L:K.333, L:K.333, L:T.334, L:N.335, L:N.335, L:E.372, L:N.414, L:C.447, L:G.452

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.333, T.334, D.371 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.334 MG.6: 4 residues within 4Å: Chain D: T.334, D.371, E.372 Ligands: ANP.5 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.334, D:E.372 MG.9: 4 residues within 4Å: Chain F: T.334, D.371, E.372 Ligands: ANP.8 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.334, F:E.372 MG.11: 2 residues within 4Å: Chain G: T.334 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.334 MG.13: 3 residues within 4Å: Chain H: T.334, E.372 Ligands: ANP.12 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.334 MG.15: 2 residues within 4Å: Chain I: T.334 Ligands: ANP.14 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.334 MG.17: 3 residues within 4Å: Chain J: T.334, E.372 Ligands: ANP.16 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:T.334, J:E.372 MG.20: 2 residues within 4Å: Chain L: T.334 Ligands: ANP.19 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Structural and functional studies of the main replication protein NS1 of human parvovirus B19. Nucleic Acids Res. (2025)

Release Date

2025-07-09

Peptides

Non-structural protein 1: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Non-structural protein 1

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