SMTL ID : 3dpr.3 (3 other biounits)

Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-6-6-6-6-6-mer

Ligands

6 x DAO: LAURIC ACID(Non-covalent)

DAO.1: 9 residues within 4Å: Chain A: I.99, N.100, L.101, Q.102, S.121, I.123, Y.145, F.180, N.211 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.99, A:I.123, A:I.123, A:Y.145, A:F.180, A:N.211 Hydrogen bonds: A:L.101, A:Q.102, A:Q.102, A:N.211 Salt bridges: A:H.259 DAO.3: 9 residues within 4Å: Chain F: I.99, N.100, L.101, Q.102, S.121, I.123, Y.145, F.180, N.211 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:I.99, F:I.123, F:I.123, F:Y.145, F:F.180, F:N.211 Hydrogen bonds: F:L.101, F:Q.102, F:Q.102, F:N.211 Salt bridges: F:H.259 DAO.5: 9 residues within 4Å: Chain K: I.99, N.100, L.101, Q.102, S.121, I.123, Y.145, F.180, N.211 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:I.99, K:I.123, K:I.123, K:Y.145, K:F.180, K:N.211 Hydrogen bonds: K:L.101, K:Q.102, K:Q.102, K:N.211 Salt bridges: K:H.259 DAO.7: 9 residues within 4Å: Chain P: I.99, N.100, L.101, Q.102, S.121, I.123, Y.145, F.180, N.211 11 PLIP interactions: 11 interactions with chain P Hydrophobic interactions: P:I.99, P:I.123, P:I.123, P:Y.145, P:F.180, P:N.211 Hydrogen bonds: P:L.101, P:Q.102, P:Q.102, P:N.211 Salt bridges: P:H.259 DAO.9: 9 residues within 4Å: Chain U: I.99, N.100, L.101, Q.102, S.121, I.123, Y.145, F.180, N.211 11 PLIP interactions: 11 interactions with chain U Hydrophobic interactions: U:I.99, U:I.123, U:I.123, U:Y.145, U:F.180, U:N.211 Hydrogen bonds: U:L.101, U:Q.102, U:Q.102, U:N.211 Salt bridges: U:H.259 DAO.11: 9 residues within 4Å: Chain Z: I.99, N.100, L.101, Q.102, S.121, I.123, Y.145, F.180, N.211 11 PLIP interactions: 11 interactions with chain Z Hydrophobic interactions: Z:I.99, Z:I.123, Z:I.123, Z:Y.145, Z:F.180, Z:N.211 Hydrogen bonds: Z:L.101, Z:Q.102, Z:Q.102, Z:N.211 Salt bridges: Z:H.259

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain E: W.20, D.23, E.25, N.26, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:W.20, E:D.23, E:E.25, E:D.27, E:D.33 CA.4: 7 residues within 4Å: Chain J: W.20, D.23, E.25, N.26, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:W.20, J:D.23, J:E.25, J:D.27, J:D.33 CA.6: 7 residues within 4Å: Chain O: W.20, D.23, E.25, N.26, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:W.20, O:D.23, O:E.25, O:D.27, O:D.33 CA.8: 7 residues within 4Å: Chain T: W.20, D.23, E.25, N.26, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:W.20, T:D.23, T:E.25, T:D.27, T:D.33 CA.10: 7 residues within 4Å: Chain Y: W.20, D.23, E.25, N.26, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain Y Metal complexes: Y:W.20, Y:D.23, Y:E.25, Y:D.27, Y:D.33 CA.12: 7 residues within 4Å: Chain 3: W.20, D.23, E.25, N.26, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain 3 Metal complexes: 3:W.20, 3:D.23, 3:E.25, 3:D.27, 3:D.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Querol-Audi, J. et al., Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition. Febs Lett. (2009)

Release Date

2009-04-07

Peptides

Protein VP1: AFKPUZ
Protein VP2: BGLQV0
Protein VP3: CHMRW1
Protein VP4: DINSX2
LDL-receptor class A 3: EJOTY3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
A

K
A

P
A

U
A

Z
A

B
B

G
B

L
B

Q
B

V
B

0
B

C
C

H
C

M
C

R
C

W
C

1
C

D
D

I
D

N
D

S
D

X
D

2
D

E
E

J
E

O
E

T
E

Y
E

3
E

Protein VP1

Protein VP2

Protein VP3

Protein VP4

LDL-receptor class A 3

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