SMTL ID : 7urn.1

Structure of HIV-1 capsid declination

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-35-mer

Ligands

10 x IHP: INOSITOL HEXAKISPHOSPHATE(Covalent)(Non-covalent)

IHP.1: 15 residues within 4Å: Chain 2: S.16, R.18, T.19 Chain A: S.16, R.18 Chain H: S.16, R.18 Chain O: S.16, R.18 Chain V: S.16, R.18 Ligands: IHP.3, IHP.5, IHP.7, IHP.9 13 PLIP interactions: 3 interactions with chain O, 2 interactions with chain 2, 2 interactions with chain H, 3 interactions with chain A, 3 interactions with chain V Hydrogen bonds: O:S.16, 2:S.16, H:S.16, A:S.16, V:S.16 Salt bridges: O:R.18, O:R.18, 2:R.18, H:R.18, A:R.18, A:R.18, V:R.18, V:R.18 IHP.2: 17 residues within 4Å: Chain 2: R.18, A.22, K.25 Chain A: R.18, A.22, K.25 Chain H: A.22, K.25 Chain O: A.22, K.25 Chain V: R.18, A.22, K.25 Ligands: IHP.4, IHP.6, IHP.8, IHP.10 14 PLIP interactions: 2 interactions with chain H, 4 interactions with chain 2, 3 interactions with chain A, 2 interactions with chain V, 3 interactions with chain O Salt bridges: H:K.25, H:K.25, 2:R.18, 2:K.25, 2:K.25, A:K.25, A:K.25, A:K.25, V:R.18, V:K.25, O:K.25, O:K.25, O:K.25 Hydrogen bonds: 2:R.18 IHP.3: 15 residues within 4Å: Chain 2: S.16, R.18 Chain A: S.16, R.18, T.19 Chain H: S.16, R.18 Chain O: S.16, R.18 Chain V: S.16, R.18 Ligands: IHP.1, IHP.5, IHP.7, IHP.9 13 PLIP interactions: 2 interactions with chain O, 3 interactions with chain 2, 3 interactions with chain H, 2 interactions with chain A, 3 interactions with chain V Hydrogen bonds: O:S.16, 2:S.16, H:S.16, A:S.16, V:S.16 Salt bridges: O:R.18, 2:R.18, 2:R.18, H:R.18, H:R.18, A:R.18, V:R.18, V:R.18 IHP.4: 17 residues within 4Å: Chain 2: R.18, A.22, K.25 Chain A: R.18, A.22, K.25 Chain H: R.18, A.22, K.25 Chain O: A.22, K.25 Chain V: A.22, K.25 Ligands: IHP.2, IHP.6, IHP.8, IHP.10 13 PLIP interactions: 3 interactions with chain H, 2 interactions with chain 2, 3 interactions with chain A, 3 interactions with chain V, 2 interactions with chain O Salt bridges: H:K.25, H:K.25, H:K.25, 2:R.18, 2:K.25, A:R.18, A:K.25, A:K.25, V:K.25, V:K.25, V:K.25, O:K.25, O:K.25 IHP.5: 15 residues within 4Å: Chain 2: S.16, R.18 Chain A: S.16, R.18 Chain H: S.16, R.18, T.19 Chain O: S.16, R.18 Chain V: S.16, R.18 Ligands: IHP.1, IHP.3, IHP.7, IHP.9 13 PLIP interactions: 3 interactions with chain O, 3 interactions with chain 2, 2 interactions with chain H, 3 interactions with chain A, 2 interactions with chain V Hydrogen bonds: O:S.16, 2:S.16, H:S.16, A:S.16, V:S.16 Salt bridges: O:R.18, O:R.18, 2:R.18, 2:R.18, H:R.18, A:R.18, A:R.18, V:R.18 IHP.6: 17 residues within 4Å: Chain 2: A.22, K.25 Chain A: R.18, A.22, K.25 Chain H: R.18, A.22, K.25 Chain O: R.18, A.22, K.25 Chain V: A.22, K.25 Ligands: IHP.2, IHP.4, IHP.8, IHP.10 13 PLIP interactions: 3 interactions with chain H, 3 interactions with chain 2, 2 interactions with chain A, 2 interactions with chain V, 3 interactions with chain O Salt bridges: H:R.18, H:K.25, H:K.25, 2:K.25, 2:K.25, 2:K.25, A:R.18, A:K.25, V:K.25, V:K.25, O:K.25, O:K.25, O:K.25 IHP.7: 15 residues within 4Å: Chain 2: S.16, R.18 Chain A: S.16, R.18 Chain H: S.16, R.18 Chain O: S.16, R.18, T.19 Chain V: S.16, R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.9 13 PLIP interactions: 2 interactions with chain O, 2 interactions with chain 2, 3 interactions with chain H, 3 interactions with chain A, 3 interactions with chain V Hydrogen bonds: O:S.16, 2:S.16, H:S.16, A:S.16, V:S.16 Salt bridges: O:R.18, 2:R.18, H:R.18, H:R.18, A:R.18, A:R.18, V:R.18, V:R.18 IHP.8: 17 residues within 4Å: Chain 2: A.22, K.25 Chain A: A.22, K.25 Chain H: R.18, A.22, K.25 Chain O: R.18, A.22, K.25 Chain V: R.18, A.22, K.25 Ligands: IHP.2, IHP.4, IHP.6, IHP.10 13 PLIP interactions: 3 interactions with chain O, 2 interactions with chain H, 2 interactions with chain 2, 3 interactions with chain A, 3 interactions with chain V Salt bridges: O:R.18, O:K.25, O:K.25, H:R.18, H:K.25, 2:K.25, 2:K.25, A:K.25, A:K.25, A:K.25, V:K.25, V:K.25, V:K.25 IHP.9: 15 residues within 4Å: Chain 2: S.16, R.18 Chain A: S.16, R.18 Chain H: S.16, R.18 Chain O: S.16, R.18 Chain V: S.16, R.18, T.19 Ligands: IHP.1, IHP.3, IHP.5, IHP.7 13 PLIP interactions: 3 interactions with chain O, 3 interactions with chain 2, 3 interactions with chain H, 2 interactions with chain A, 2 interactions with chain V Hydrogen bonds: O:S.16, 2:S.16, H:S.16, A:S.16, V:S.16 Salt bridges: O:R.18, O:R.18, 2:R.18, 2:R.18, H:R.18, H:R.18, A:R.18, V:R.18 IHP.10: 17 residues within 4Å: Chain 2: R.18, A.22, K.25 Chain A: A.22, K.25 Chain H: A.22, K.25 Chain O: R.18, A.22, K.25 Chain V: R.18, A.22, K.25 Ligands: IHP.2, IHP.4, IHP.6, IHP.8 14 PLIP interactions: 2 interactions with chain O, 3 interactions with chain H, 3 interactions with chain 2, 2 interactions with chain A, 4 interactions with chain V Salt bridges: O:R.18, O:K.25, H:K.25, H:K.25, H:K.25, 2:K.25, 2:K.25, 2:K.25, A:K.25, A:K.25, V:R.18, V:K.25, V:K.25 Hydrogen bonds: V:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schirra, R.T. et al., A molecular switch modulates assembly and host factor binding of the HIV-1 capsid. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-02-15

Peptides

HIV-1 capsid protein: ABCDEFGHIJKLMNOPQRSTUVWXYZ012345678

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
M

D
N

E
O

F
P

G
Q

H
A

I
L

J
M

K
N

L
O

M
P

N
Q

O
A

P
L

Q
M

R
N

S
O

T
P

U
Q

V
A

W
L

X
M

Y
N

Z
O

0
P

1
Q

2
A

3
L

4
M

5
N

6
O

7
P

8
Q

HIV-1 capsid protein

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