SMTL ID : 1k5m.3 (4 other biounits)

Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 13 residues within 4Å: Chain A: L.106, S.107, L.116, V.122, Y.128, Y.152, V.176, F.186, V.188, Y.197, N.198, C.199 Chain C: A.24 16 PLIP interactions: 1 interactions with chain C, 15 interactions with chain A Hydrophobic interactions: C:A.24, A:L.106, A:Y.152, A:Y.152, A:Y.152, A:Y.152, A:V.176, A:F.186, A:F.186, A:V.188, A:Y.197, A:Y.197 Hydrogen bonds: A:L.106, A:S.107 Water bridges: A:S.107, A:N.219 SPH.2: 13 residues within 4Å: Chain E: L.106, S.107, L.116, V.122, Y.128, Y.152, V.176, F.186, V.188, Y.197, N.198, C.199 Chain G: A.24 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:L.106, E:Y.152, E:Y.152, E:Y.152, E:Y.152, E:V.176, E:F.186, E:F.186, E:V.188, E:Y.197, E:Y.197, G:A.24 Hydrogen bonds: E:L.106, E:S.107 Water bridges: E:S.107, E:N.219 SPH.3: 13 residues within 4Å: Chain I: L.106, S.107, L.116, V.122, Y.128, Y.152, V.176, F.186, V.188, Y.197, N.198, C.199 Chain K: A.24 16 PLIP interactions: 15 interactions with chain I, 1 interactions with chain K Hydrophobic interactions: I:L.106, I:Y.152, I:Y.152, I:Y.152, I:Y.152, I:V.176, I:F.186, I:F.186, I:V.188, I:Y.197, I:Y.197, K:A.24 Hydrogen bonds: I:L.106, I:S.107 Water bridges: I:S.107, I:N.219 SPH.4: 13 residues within 4Å: Chain M: L.106, S.107, L.116, V.122, Y.128, Y.152, V.176, F.186, V.188, Y.197, N.198, C.199 Chain O: A.24 16 PLIP interactions: 15 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: M:L.106, M:Y.152, M:Y.152, M:Y.152, M:Y.152, M:V.176, M:F.186, M:F.186, M:V.188, M:Y.197, M:Y.197, O:A.24 Hydrogen bonds: M:L.106, M:S.107 Water bridges: M:S.107, M:N.219 SPH.5: 13 residues within 4Å: Chain Q: L.106, S.107, L.116, V.122, Y.128, Y.152, V.176, F.186, V.188, Y.197, N.198, C.199 Chain S: A.24 16 PLIP interactions: 15 interactions with chain Q, 1 interactions with chain S Hydrophobic interactions: Q:L.106, Q:Y.152, Q:Y.152, Q:Y.152, Q:Y.152, Q:V.176, Q:F.186, Q:F.186, Q:V.188, Q:Y.197, Q:Y.197, S:A.24 Hydrogen bonds: Q:L.106, Q:S.107 Water bridges: Q:S.107, Q:N.219 SPH.6: 13 residues within 4Å: Chain U: L.106, S.107, L.116, V.122, Y.128, Y.152, V.176, F.186, V.188, Y.197, N.198, C.199 Chain W: A.24 16 PLIP interactions: 15 interactions with chain U, 1 interactions with chain W Hydrophobic interactions: U:L.106, U:Y.152, U:Y.152, U:Y.152, U:Y.152, U:V.176, U:F.186, U:F.186, U:V.188, U:Y.197, U:Y.197, W:A.24 Hydrogen bonds: U:L.106, U:S.107 Water bridges: U:S.107, U:N.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, J. et al., Crystal Structure of a Human Rhinovirus that Displays Part of the HIV-1 V3 Loop and Induces Neutralizing Antibodies against HIV-1. Structure (2002)

Release Date

2002-07-17

Peptides

COAT PROTEIN VP1 (P1D): AEIMQU
CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120: BFJNRV
COAT PROTEIN VP3 (P1C): CGKOSW
COAT PROTEIN VP4 (P1A): DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

U
A

B
B

F
B

J
B

N
B

R
B

V
B

C
C

G
C

K
C

O
C

S
C

W
C

D
D

H
D

L
D

P
D

T
D

X
D

COAT PROTEIN VP1 (P1D)

CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120

COAT PROTEIN VP3 (P1C)

COAT PROTEIN VP4 (P1A)

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