SMTL ID : 8pdq.1

11-mer ring of HMPV N-RNA bound to the C-terminal region of P

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-11-mer

Ligands

11 x ASP- ILE- TYR- GLN- LEU- ILE- MET: Phosphoprotein(Non-covalent)

ASP-ILE-TYR-GLN-LEU-ILE-MET.1: 14 residues within 4Å: Chain A: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.103, A:L.111, A:R.132, A:A.136 Hydrogen bonds: A:N.105, A:N.106, A:R.132, A:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.3: 14 residues within 4Å: Chain B: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.103, B:L.111, B:R.132, B:A.136 Hydrogen bonds: B:N.105, B:N.106, B:R.132, B:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.5: 14 residues within 4Å: Chain C: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.103, C:L.111, C:R.132, C:A.136 Hydrogen bonds: C:N.105, C:N.106, C:R.132, C:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.7: 14 residues within 4Å: Chain D: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.103, D:L.111, D:R.132, D:A.136 Hydrogen bonds: D:N.105, D:N.106, D:R.132, D:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.9: 14 residues within 4Å: Chain E: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.103, E:L.111, E:R.132, E:A.136 Hydrogen bonds: E:N.105, E:N.106, E:R.132, E:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.11: 14 residues within 4Å: Chain F: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.103, F:L.111, F:R.132, F:A.136 Hydrogen bonds: F:N.105, F:N.106, F:R.132, F:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.13: 14 residues within 4Å: Chain G: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:I.103, G:L.111, G:R.132, G:A.136 Hydrogen bonds: G:N.105, G:N.106, G:R.132, G:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.15: 14 residues within 4Å: Chain H: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:I.103, H:L.111, H:R.132, H:A.136 Hydrogen bonds: H:N.105, H:N.106, H:R.132, H:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.17: 14 residues within 4Å: Chain I: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:I.103, I:L.111, I:R.132, I:A.136 Hydrogen bonds: I:N.105, I:N.106, I:R.132, I:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.19: 14 residues within 4Å: Chain J: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain J Hydrophobic interactions: J:I.103, J:L.111, J:R.132, J:A.136 Hydrogen bonds: J:N.105, J:N.106, J:R.132, J:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.21: 14 residues within 4Å: Chain K: L.46, E.50, Y.53, I.103, K.104, N.105, N.106, L.111, K.129, R.132, M.135, A.136, P.152, S.153 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:I.103, K:L.111, K:R.132, K:A.136 Hydrogen bonds: K:N.105, K:N.106, K:R.132, K:S.153

11 x C- C- C- C- C- C- C: RNA(Non-covalent)

C-C-C-C-C-C-C.2: 31 residues within 4Å: Chain A: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain K: R.186, R.189, V.190, L.243, N.246, Q.250 Ligands: C-C-C-C-C-C-C.4, C-C-C-C-C-C-C.4, C-C-C-C-C-C-C.22 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.4: 31 residues within 4Å: Chain A: R.186, R.189, V.190, L.243, N.246, Q.250 Chain B: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.2, C-C-C-C-C-C-C.6, C-C-C-C-C-C-C.6 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.6: 31 residues within 4Å: Chain B: R.186, R.189, V.190, L.243, N.246, Q.250 Chain C: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.4, C-C-C-C-C-C-C.8, C-C-C-C-C-C-C.8 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.8: 31 residues within 4Å: Chain C: R.186, R.189, V.190, L.243, N.246, Q.250 Chain D: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.6, C-C-C-C-C-C-C.10, C-C-C-C-C-C-C.10 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.10: 31 residues within 4Å: Chain D: R.186, R.189, V.190, L.243, N.246, Q.250 Chain E: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.8, C-C-C-C-C-C-C.12, C-C-C-C-C-C-C.12 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.12: 31 residues within 4Å: Chain E: R.186, R.189, V.190, L.243, N.246, Q.250 Chain F: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.10, C-C-C-C-C-C-C.14, C-C-C-C-C-C-C.14 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.14: 31 residues within 4Å: Chain F: R.186, R.189, V.190, L.243, N.246, Q.250 Chain G: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.12, C-C-C-C-C-C-C.16, C-C-C-C-C-C-C.16 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.16: 31 residues within 4Å: Chain G: R.186, R.189, V.190, L.243, N.246, Q.250 Chain H: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.14, C-C-C-C-C-C-C.18, C-C-C-C-C-C-C.18 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.18: 31 residues within 4Å: Chain H: R.186, R.189, V.190, L.243, N.246, Q.250 Chain I: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.16, C-C-C-C-C-C-C.20, C-C-C-C-C-C-C.20 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.20: 31 residues within 4Å: Chain I: R.186, R.189, V.190, L.243, N.246, Q.250 Chain J: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.18, C-C-C-C-C-C-C.22, C-C-C-C-C-C-C.22 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.22: 31 residues within 4Å: Chain J: R.186, R.189, V.190, L.243, N.246, Q.250 Chain K: K.171, A.173, S.174, V.178, T.182, R.185, R.186, R.189, Q.250, G.255, Q.256, T.257, W.261, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Ligands: C-C-C-C-C-C-C.2, C-C-C-C-C-C-C.2, C-C-C-C-C-C-C.20 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitehead, J.D. et al., Structure of the N-RNA/P interface indicates mode of L/P recruitment to the nucleocapsid of human metapneumovirus. Nat Commun (2023)

Release Date

2023-12-06

Peptides

Nucleoprotein: ABCDEFGHIJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

Nucleoprotein

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