SMTL ID : 8pdr.1

Rigid body fit of assembled HMPV N-RNA spiral 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: 12 residues within 4Å: Chain A: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.46, A:I.103, A:L.111, A:R.132, A:K.133 Hydrogen bonds: A:R.132, A:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.2: 12 residues within 4Å: Chain B: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.46, B:I.103, B:L.111, B:R.132, B:K.133 Hydrogen bonds: B:R.132, B:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.3: 12 residues within 4Å: Chain C: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.46, C:I.103, C:L.111, C:R.132, C:K.133 Hydrogen bonds: C:R.132, C:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.4: 12 residues within 4Å: Chain D: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.46, D:I.103, D:L.111, D:R.132, D:K.133 Hydrogen bonds: D:R.132, D:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.5: 12 residues within 4Å: Chain E: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.46, E:I.103, E:L.111, E:R.132, E:K.133 Hydrogen bonds: E:R.132, E:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.6: 12 residues within 4Å: Chain F: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:L.46, F:I.103, F:L.111, F:R.132, F:K.133 Hydrogen bonds: F:R.132, F:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.7: 12 residues within 4Å: Chain G: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:L.46, G:I.103, G:L.111, G:R.132, G:K.133 Hydrogen bonds: G:R.132, G:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.8: 12 residues within 4Å: Chain H: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:L.46, H:I.103, H:L.111, H:R.132, H:K.133 Hydrogen bonds: H:R.132, H:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.9: 12 residues within 4Å: Chain I: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:L.46, I:I.103, I:L.111, I:R.132, I:K.133 Hydrogen bonds: I:R.132, I:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.10: 12 residues within 4Å: Chain J: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:L.46, J:I.103, J:L.111, J:R.132, J:K.133 Hydrogen bonds: J:R.132, J:S.153 ASP-ILE-TYR-GLN-LEU-ILE-MET.11: 12 residues within 4Å: Chain K: L.46, Y.53, I.103, N.106, L.111, R.132, K.133, M.135, A.136, R.151, P.152, S.153 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:L.46, K:I.103, K:L.111, K:R.132, K:K.133 Hydrogen bonds: 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.12: 25 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, H.303, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain B: N.317 Ligands: C-C-C-C-C-C-C.13 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.13: 32 residues within 4Å: Chain A: R.186, R.189, V.190, S.242, L.243, N.246 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, H.303, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain C: N.317 Ligands: C-C-C-C-C-C-C.12, C-C-C-C-C-C-C.14 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.14: 33 residues within 4Å: Chain B: R.186, R.189, V.190, S.242, L.243, N.246 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, H.303, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain D: N.317 Ligands: C-C-C-C-C-C-C.13, C-C-C-C-C-C-C.15, C-C-C-C-C-C-C.15 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.15: 35 residues within 4Å: Chain C: R.186, R.189, V.190, S.242, L.243, N.246, I.247, 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, H.303, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain E: N.317 Ligands: C-C-C-C-C-C-C.14, 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: 34 residues within 4Å: Chain D: R.186, R.189, V.190, S.242, 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, H.303, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain F: N.317 Ligands: C-C-C-C-C-C-C.15, C-C-C-C-C-C-C.17, C-C-C-C-C-C-C.17 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.17: 34 residues within 4Å: Chain E: R.186, R.189, V.190, S.242, 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, H.303, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain G: N.317 Ligands: C-C-C-C-C-C-C.16, 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: 34 residues within 4Å: Chain F: R.186, R.189, V.190, S.242, 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, H.303, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain H: N.317 Ligands: C-C-C-C-C-C-C.17, C-C-C-C-C-C-C.19, C-C-C-C-C-C-C.19 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.19: 33 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, H.303, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain I: N.317 Ligands: C-C-C-C-C-C-C.18, 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: 33 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, H.303, S.314, A.316, I.334, I.335, G.336, M.337, Y.338, R.339, G.340 Chain J: N.317 Ligands: C-C-C-C-C-C-C.19, C-C-C-C-C-C-C.21, C-C-C-C-C-C-C.21 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.21: 32 residues within 4Å: Chain I: R.186, R.189, V.190, S.242, 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, H.303, 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.20, C-C-C-C-C-C-C.22 Protein-ligand interaction information (PLIP) not available C-C-C-C-C-C-C.22: 30 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, H.303, 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.21 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
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

Nucleoprotein

Related Entries With Identical Sequence