SMTL ID : 9d6d.1

Gag CA-SP1 immature lattice bound with Lenacapavir from enveloped virus like particles

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

18 x QNG: Lenacapavir(Non-covalent)

QNG.1: 24 residues within 4Å: Chain A: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain B: I.5, S.6, P.7, R.8, L.10, N.11 Chain D: E.69, R.72 17 PLIP interactions: 2 interactions with chain B, 14 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:P.7, A:Q.40, A:L.46, A:L.46, A:A.95, A:T.97 pi-Cation interactions: B:R.8, A:K.60, A:K.60 Hydrogen bonds: A:N.47, A:N.47, A:K.60, A:N.64, A:N.64 Halogen bonds: A:N.47, A:Q.53, D:E.69 QNG.2: 23 residues within 4Å: Chain A: I.5, S.6, P.7, R.8, N.11 Chain B: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain C: E.69, R.72 19 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:Q.40, B:L.46, B:L.46, B:A.95, B:T.97, A:P.7 Hydrogen bonds: B:N.47, B:N.47, B:K.60, B:N.64, B:N.64 pi-Cation interactions: B:K.60, B:K.60, A:R.8 Halogen bonds: B:N.47, B:N.47, B:Q.53, B:Q.53, C:E.69 QNG.4: 15 residues within 4Å: Chain C: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, T.97, Y.120 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Q.40, C:L.46, C:L.46, C:Q.53, C:T.97 Hydrogen bonds: C:N.47, C:N.47, C:K.60, C:N.64, C:N.64 pi-Cation interactions: C:K.60, C:K.60 Halogen bonds: C:N.47, C:N.47, C:Q.53 QNG.6: 24 residues within 4Å: Chain D: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain E: I.5, S.6, P.7, R.8, L.10, N.11 Chain G: E.69, R.72 17 PLIP interactions: 1 interactions with chain G, 14 interactions with chain D, 2 interactions with chain E Halogen bonds: G:E.69, D:N.47, D:Q.53 Hydrophobic interactions: D:Q.40, D:L.46, D:L.46, D:A.95, D:T.97, E:P.7 Hydrogen bonds: D:N.47, D:N.47, D:K.60, D:N.64, D:N.64 pi-Cation interactions: D:K.60, D:K.60, E:R.8 QNG.7: 22 residues within 4Å: Chain D: I.5, S.6, P.7, R.8, N.11 Chain E: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, T.97, Y.120 Chain F: E.69, R.72 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:Q.40, E:L.46, E:L.46, E:Q.53, E:M.56, E:A.95, E:T.97, D:P.7 Hydrogen bonds: E:N.47, E:N.47, E:K.60, E:N.64, E:N.64 pi-Cation interactions: E:K.60, E:K.60, D:R.8 Halogen bonds: E:N.47, E:N.47, E:Q.53, E:Q.53 QNG.9: 15 residues within 4Å: Chain F: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, T.97, Y.120 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:Q.40, F:N.43, F:L.46, F:L.46, F:Q.53, F:A.95, F:T.97 Hydrogen bonds: F:N.47, F:N.47, F:K.60, F:N.64, F:N.64 pi-Cation interactions: F:K.60, F:K.60 Halogen bonds: F:N.47, F:N.47, F:Q.53, F:M.56 QNG.10: 23 residues within 4Å: Chain G: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain H: I.5, S.6, P.7, R.8, N.11 Chain J: E.69, R.72 16 PLIP interactions: 13 interactions with chain G, 1 interactions with chain J, 2 interactions with chain H Hydrophobic interactions: G:Q.40, G:L.46, G:L.46, G:A.95, G:T.97, H:P.7 Hydrogen bonds: G:N.47, G:N.47, G:K.60, G:N.64 pi-Cation interactions: G:K.60, G:K.60, H:R.8 Halogen bonds: G:N.47, G:Q.53, J:E.69 QNG.11: 23 residues within 4Å: Chain G: I.5, S.6, P.7, R.8, N.11 Chain H: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain I: E.69, R.72 20 PLIP interactions: 1 interactions with chain I, 17 interactions with chain H, 2 interactions with chain G Halogen bonds: I:E.69, H:N.47, H:N.47 Hydrophobic interactions: H:Q.40, H:N.43, H:L.46, H:L.46, H:Q.53, H:M.56, H:A.95, H:T.97, G:P.7 Hydrogen bonds: H:N.47, H:N.47, H:K.60, H:N.64, H:N.64 pi-Cation interactions: H:K.60, H:K.60, G:R.8 QNG.13: 15 residues within 4Å: Chain I: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, T.97, Y.120 17 PLIP interactions: 17 interactions with chain I Hydrophobic interactions: I:Q.40, I:N.43, I:L.46, I:L.46, I:A.95, I:T.97 Hydrogen bonds: I:N.47, I:N.47, I:K.60, I:N.64, I:N.64 pi-Cation interactions: I:K.60, I:K.60 Halogen bonds: I:N.47, I:N.47, I:Q.53, I:M.56 QNG.14: 24 residues within 4Å: Chain J: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain K: I.5, S.6, P.7, R.8, L.10, N.11 Chain M: E.69, R.72 17 PLIP interactions: 2 interactions with chain K, 1 interactions with chain M, 14 interactions with chain J Hydrophobic interactions: K:P.7, J:Q.40, J:L.46, J:L.46, J:A.95, J:T.97 pi-Cation interactions: K:R.8, J:K.60, J:K.60 Halogen bonds: M:E.69, J:N.47, J:Q.53 Hydrogen bonds: J:N.47, J:N.47, J:K.60, J:N.64, J:N.64 QNG.15: 22 residues within 4Å: Chain J: I.5, S.6, P.7, R.8, N.11 Chain K: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, T.97, Y.120 Chain L: E.69, R.72 19 PLIP interactions: 16 interactions with chain K, 1 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: K:Q.40, K:L.46, K:L.46, K:A.95, K:T.97, J:P.7 Hydrogen bonds: K:N.47, K:N.47, K:K.60, K:N.64, K:N.64 pi-Cation interactions: K:K.60, K:K.60, J:R.8 Halogen bonds: K:N.47, K:N.47, K:Q.53, K:Q.53, L:E.69 QNG.17: 15 residues within 4Å: Chain L: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, T.97, Y.120 15 PLIP interactions: 15 interactions with chain L Hydrophobic interactions: L:Q.40, L:L.46, L:L.46, L:A.95, L:T.97 Hydrogen bonds: L:N.47, L:N.47, L:K.60, L:N.64, L:N.64 pi-Cation interactions: L:K.60, L:K.60 Halogen bonds: L:N.47, L:N.47, L:Q.53 QNG.18: 24 residues within 4Å: Chain M: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain N: I.5, S.6, P.7, R.8, L.10, N.11 Chain P: E.69, R.72 19 PLIP interactions: 1 interactions with chain P, 16 interactions with chain M, 2 interactions with chain N Halogen bonds: P:E.69, M:N.47, M:Q.53, M:Q.57, M:N.64 Hydrophobic interactions: M:Q.40, M:L.46, M:L.46, M:A.95, M:T.97, N:P.7 Hydrogen bonds: M:N.47, M:N.47, M:K.60, M:N.64, M:N.64 pi-Cation interactions: M:K.60, M:K.60, N:R.8 QNG.19: 23 residues within 4Å: Chain M: I.5, S.6, P.7, R.8, N.11 Chain N: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain O: E.69, R.72 20 PLIP interactions: 1 interactions with chain O, 17 interactions with chain N, 2 interactions with chain M Halogen bonds: O:E.69, N:N.47, N:N.47, N:Q.53 Hydrophobic interactions: N:Q.40, N:L.46, N:L.46, N:Q.53, N:M.56, N:A.95, N:T.97, M:P.7 Hydrogen bonds: N:N.47, N:N.47, N:K.60, N:N.64, N:N.64 pi-Cation interactions: N:K.60, N:K.60, M:R.8 QNG.21: 16 residues within 4Å: Chain O: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 15 PLIP interactions: 15 interactions with chain O Hydrophobic interactions: O:Q.40, O:L.46, O:L.46, O:A.95, O:T.97 Hydrogen bonds: O:N.47, O:N.47, O:K.60, O:N.64, O:N.64 pi-Cation interactions: O:K.60, O:K.60 Halogen bonds: O:N.47, O:N.47, O:Q.53 QNG.22: 24 residues within 4Å: Chain A: E.69, R.72 Chain P: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain Q: I.5, S.6, P.7, R.8, L.10, N.11 17 PLIP interactions: 14 interactions with chain P, 2 interactions with chain Q, 1 interactions with chain A Hydrophobic interactions: P:Q.40, P:L.46, P:L.46, P:A.95, P:T.97, Q:P.7 Hydrogen bonds: P:N.47, P:N.47, P:K.60, P:N.64, P:N.64 pi-Cation interactions: P:K.60, P:K.60, Q:R.8 Halogen bonds: P:N.47, P:Q.53, A:E.69 QNG.23: 23 residues within 4Å: Chain P: I.5, S.6, P.7, R.8, N.11 Chain Q: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, G.96, T.97, Y.120 Chain R: E.69, R.72 19 PLIP interactions: 17 interactions with chain Q, 2 interactions with chain P Hydrophobic interactions: Q:Q.40, Q:N.43, Q:L.46, Q:L.46, Q:Q.53, Q:M.56, Q:A.95, Q:T.97, P:P.7 Hydrogen bonds: Q:N.47, Q:N.47, Q:K.60, Q:N.64, Q:N.64 pi-Cation interactions: Q:K.60, Q:K.60, P:R.8 Halogen bonds: Q:N.47, Q:N.47 QNG.25: 15 residues within 4Å: Chain R: Q.40, N.43, T.44, L.46, N.47, Q.53, M.56, Q.57, L.59, K.60, I.63, N.64, A.95, T.97, Y.120 17 PLIP interactions: 17 interactions with chain R Hydrophobic interactions: R:Q.40, R:N.43, R:L.46, R:L.46, R:A.95, R:T.97 Hydrogen bonds: R:N.47, R:N.47, R:K.60, R:N.64, R:N.64 pi-Cation interactions: R:K.60, R:K.60 Halogen bonds: R:N.47, R:N.47, R:Q.53, R:M.56

7 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.3: 4 residues within 4Å: Chain B: K.148, K.217 Chain C: K.148, K.217 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Salt bridges: B:K.148, B:K.217, B:K.217, C:K.148, C:K.217 IHP.5: 12 residues within 4Å: Chain A: K.148, K.217 Chain D: K.148, K.217 Chain G: K.148, K.217 Chain J: K.148, K.217 Chain M: K.148, K.217 Chain P: K.148, K.217 22 PLIP interactions: 4 interactions with chain J, 3 interactions with chain G, 4 interactions with chain P, 4 interactions with chain A, 3 interactions with chain M, 4 interactions with chain D Salt bridges: J:K.148, J:K.148, J:K.217, J:K.217, G:K.148, G:K.148, G:K.217, P:K.148, P:K.148, P:K.217, P:K.217, A:K.148, A:K.148, A:K.217, A:K.217, M:K.148, M:K.148, M:K.217, D:K.148, D:K.148, D:K.217, D:K.217 IHP.8: 4 residues within 4Å: Chain E: K.148, K.217 Chain F: K.148, K.217 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain E Salt bridges: F:K.148, F:K.217, E:K.148, E:K.148, E:K.217, E:K.217 IHP.12: 4 residues within 4Å: Chain H: K.148, K.217 Chain I: K.148, K.217 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain H Salt bridges: I:K.148, I:K.148, I:K.217, H:K.148, H:K.217, H:K.217 IHP.16: 4 residues within 4Å: Chain K: K.148, K.217 Chain L: K.148, K.217 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain K Salt bridges: L:K.148, L:K.217, K:K.148, K:K.217, K:K.217 IHP.20: 4 residues within 4Å: Chain N: K.148, K.217 Chain O: K.148, K.217 6 PLIP interactions: 3 interactions with chain N, 3 interactions with chain O Salt bridges: N:K.148, N:K.217, N:K.217, O:K.148, O:K.148, O:K.217 IHP.24: 4 residues within 4Å: Chain Q: K.148, K.217 Chain R: K.148, K.217 5 PLIP interactions: 2 interactions with chain R, 3 interactions with chain Q Salt bridges: R:K.148, R:K.217, Q:K.148, Q:K.217, Q:K.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, C. et al., Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution in situ single-particle cryo-EM. Biorxiv (2024)

Release Date

2024-10-30

Peptides

Gag polyprotein: ABCDEFGHIJKLMNOPQR

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

M
M

N
N

O
O

P
P

Q
Q

R
R

Gag polyprotein

Related Entries With Identical Sequence