SMTL ID : 9kbh.1

The structure of B19V NS1_2-570/ssDNA/AMPPNP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ANP.1: 14 residues within 4Å: Chain A: P.329, S.330, T.331, G.332, K.333, T.334, N.335, C.447, S.448, P.449, D.450, M.451, G.452 Chain F: Q.390 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.330, A:T.331, A:G.332, A:K.333, A:T.334, A:T.334, A:T.334, A:N.335, A:N.335, A:S.448, A:M.451, A:G.452 ANP.2: 21 residues within 4Å: Chain A: G.318, K.319, K.384, G.388, Q.390 Chain B: 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, L.453 Ligands: MG.3 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:P.328, B:S.330, B:T.331, B:G.332, B:K.333, B:T.334, B:T.334, B:N.335, B:N.335, B:N.414, B:N.414, B:S.448, B:D.450, B:M.451, B:L.453, A:G.388, A:Q.390 Salt bridges: A:K.319 ANP.4: 21 residues within 4Å: Chain B: G.318, K.319, G.388, G.389, Q.390, R.437 Chain C: P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, S.448, P.449, D.450, M.451, G.452, L.453 Ligands: MG.5 20 PLIP interactions: 14 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:S.330, C:T.331, C:G.332, C:K.333, C:K.333, C:K.333, C:T.334, C:N.335, C:N.335, C:N.414, C:N.414, C:P.449, C:M.451, C:G.452, B:K.319, B:K.319, B:G.388, B:Q.390, B:R.437 Salt bridges: B:K.319 ANP.6: 21 residues within 4Å: Chain C: G.318, K.319, G.389, Q.390, R.437 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.7 22 PLIP interactions: 7 interactions with chain C, 15 interactions with chain D Hydrogen bonds: C:K.319, C:K.319, C:G.388, C:Q.390, C:R.437, C:R.437, 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:N.414, D:C.447, D:S.448, D:M.451, D:G.452 Salt bridges: C:K.319 ANP.8: 20 residues within 4Å: Chain D: G.318, K.319, G.389, Q.390, R.437 Chain E: P.329, S.330, T.331, G.332, K.333, T.334, N.335, E.372, N.414, S.448, P.449, D.450, M.451, G.452 Ligands: MG.9 22 PLIP interactions: 15 interactions with chain E, 7 interactions with chain D Hydrogen bonds: E:S.330, E:T.331, E:T.331, E:G.332, E:K.333, E:K.333, E:K.333, E:T.334, E:N.335, E:N.335, E:N.414, E:N.414, E:P.449, E:M.451, E:G.452, D:K.319, D:K.319, D:G.388, D:Q.390, D:R.437, D:R.437 Salt bridges: D:K.319 ANP.10: 17 residues within 4Å: Chain E: K.319, G.388, G.389, Q.390, R.437 Chain F: P.329, S.330, T.331, G.332, K.333, T.334, N.335, N.414, S.448, P.449, G.452, L.453 14 PLIP interactions: 10 interactions with chain F, 4 interactions with chain E 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:G.452, E:G.388, E:Q.390, E:R.437 Salt bridges: E:K.319

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: T.334 Ligands: ANP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.334 MG.5: 3 residues within 4Å: Chain C: T.334, D.371 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.334 MG.7: 4 residues within 4Å: Chain D: T.334, D.371, E.372 Ligands: ANP.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.334, D:E.372 MG.9: 4 residues within 4Å: Chain E: T.334, D.371, E.372 Ligands: ANP.8 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.334, E:E.372

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Non-structural protein 1

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