SMTL ID : 6ola.1

Structure of the PCV2d virus-like particle

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-60-mer

Ligands

60 x DC- DC- DG- DG: DNA (5'-D(P*CP*CP*GP*G)-3')(Non-covalent)

DC-DC-DG-DG.1: 14 residues within 4Å: Chain A: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain E: R.112, H.113, T.114 Chain F: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.2: 14 residues within 4Å: Chain A: R.112, H.113, T.114 Chain B: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain W: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.3: 14 residues within 4Å: Chain B: R.112, H.113, T.114 Chain C: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain f: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.4: 14 residues within 4Å: Chain C: R.112, H.113, T.114 Chain D: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain n: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.5: 14 residues within 4Å: Chain 7: K.6 Chain D: R.112, H.113, T.114 Chain E: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.6: 14 residues within 4Å: Chain A: K.6 Chain F: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain J: R.112, H.113, T.114 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.7: 14 residues within 4Å: Chain 6: K.6 Chain F: R.112, H.113, T.114 Chain G: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.8: 14 residues within 4Å: Chain G: R.112, H.113, T.114 Chain H: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain u: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.9: 14 residues within 4Å: Chain H: R.112, H.113, T.114 Chain I: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain s: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.10: 14 residues within 4Å: Chain I: R.112, H.113, T.114 Chain J: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain X: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.11: 14 residues within 4Å: Chain K: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain O: R.112, H.113, T.114 Chain P: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.12: 14 residues within 4Å: Chain K: R.112, H.113, T.114 Chain L: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain b: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.13: 14 residues within 4Å: Chain L: R.112, H.113, T.114 Chain M: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain k: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.14: 14 residues within 4Å: Chain M: R.112, H.113, T.114 Chain N: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain i: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.15: 14 residues within 4Å: Chain 2: K.6 Chain N: R.112, H.113, T.114 Chain O: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.16: 14 residues within 4Å: Chain K: K.6 Chain P: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain T: R.112, H.113, T.114 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.17: 14 residues within 4Å: Chain 1: K.6 Chain P: R.112, H.113, T.114 Chain Q: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.18: 14 residues within 4Å: Chain Q: R.112, H.113, T.114 Chain R: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain p: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.19: 14 residues within 4Å: Chain R: R.112, H.113, T.114 Chain S: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain x: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.20: 14 residues within 4Å: Chain S: R.112, H.113, T.114 Chain T: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain c: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.21: 14 residues within 4Å: Chain U: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain Y: R.112, H.113, T.114 Chain Z: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.22: 14 residues within 4Å: Chain U: R.112, H.113, T.114 Chain V: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain g: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.23: 14 residues within 4Å: Chain B: K.6 Chain V: R.112, H.113, T.114 Chain W: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.24: 14 residues within 4Å: Chain J: K.6 Chain W: R.112, H.113, T.114 Chain X: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.25: 14 residues within 4Å: Chain X: R.112, H.113, T.114 Chain Y: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain r: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.26: 14 residues within 4Å: Chain 3: R.112, H.113, T.114 Chain U: K.6 Chain Z: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.27: 14 residues within 4Å: Chain 0: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain Z: R.112, H.113, T.114 Chain q: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.28: 14 residues within 4Å: Chain 0: R.112, H.113, T.114 Chain 1: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain Q: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.29: 14 residues within 4Å: Chain 1: R.112, H.113, T.114 Chain 2: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain O: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.30: 14 residues within 4Å: Chain 2: R.112, H.113, T.114 Chain 3: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain h: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.31: 14 residues within 4Å: Chain 4: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain 8: R.112, H.113, T.114 Chain 9: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.32: 14 residues within 4Å: Chain 4: R.112, H.113, T.114 Chain 5: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain v: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.33: 14 residues within 4Å: Chain 5: R.112, H.113, T.114 Chain 6: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain G: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.34: 14 residues within 4Å: Chain 6: R.112, H.113, T.114 Chain 7: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain E: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.35: 14 residues within 4Å: Chain 7: R.112, H.113, T.114 Chain 8: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain m: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.36: 14 residues within 4Å: Chain 4: K.6 Chain 9: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain d: R.112, H.113, T.114 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.37: 14 residues within 4Å: Chain 9: R.112, H.113, T.114 Chain a: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain l: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.38: 14 residues within 4Å: Chain L: K.6 Chain a: R.112, H.113, T.114 Chain b: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.39: 14 residues within 4Å: Chain T: K.6 Chain b: R.112, H.113, T.114 Chain c: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.40: 14 residues within 4Å: Chain c: R.112, H.113, T.114 Chain d: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain w: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.41: 14 residues within 4Å: Chain e: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain i: R.112, H.113, T.114 Chain j: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.42: 14 residues within 4Å: Chain C: K.6 Chain e: R.112, H.113, T.114 Chain f: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.43: 14 residues within 4Å: Chain V: K.6 Chain f: R.112, H.113, T.114 Chain g: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.44: 14 residues within 4Å: Chain 3: K.6 Chain g: R.112, H.113, T.114 Chain h: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.45: 14 residues within 4Å: Chain N: K.6 Chain h: R.112, H.113, T.114 Chain i: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.46: 14 residues within 4Å: Chain e: K.6 Chain j: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain n: R.112, H.113, T.114 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.47: 14 residues within 4Å: Chain M: K.6 Chain j: R.112, H.113, T.114 Chain k: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.48: 14 residues within 4Å: Chain a: K.6 Chain k: R.112, H.113, T.114 Chain l: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.49: 14 residues within 4Å: Chain 8: K.6 Chain l: R.112, H.113, T.114 Chain m: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.50: 14 residues within 4Å: Chain D: K.6 Chain m: R.112, H.113, T.114 Chain n: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.51: 14 residues within 4Å: Chain o: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain s: R.112, H.113, T.114 Chain t: K.6 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.52: 14 residues within 4Å: Chain R: K.6 Chain o: R.112, H.113, T.114 Chain p: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.53: 14 residues within 4Å: Chain 0: K.6 Chain p: R.112, H.113, T.114 Chain q: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.54: 14 residues within 4Å: Chain Y: K.6 Chain q: R.112, H.113, T.114 Chain r: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.55: 14 residues within 4Å: Chain I: K.6 Chain r: R.112, H.113, T.114 Chain s: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.56: 14 residues within 4Å: Chain o: K.6 Chain t: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Chain x: R.112, H.113, T.114 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.57: 14 residues within 4Å: Chain H: K.6 Chain t: R.112, H.113, T.114 Chain u: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.58: 14 residues within 4Å: Chain 5: K.6 Chain u: R.112, H.113, T.114 Chain v: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.59: 14 residues within 4Å: Chain d: K.6 Chain v: R.112, H.113, T.114 Chain w: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG.60: 14 residues within 4Å: Chain S: K.6 Chain w: R.112, H.113, T.114 Chain x: N.11, R.13, R.64, K.67, W.71, Y.121, S.123, Y.125, K.144, Y.183 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khayat, R. et al., Structural characterization of the PCV2d virus-like particle at 3.3 angstrom resolution reveals differences to PCV2a and PCV2b capsids, a tetranucleotide, and an N-terminus near the icosahedral 3-fold axes. Virology (2019)

Release Date

2019-09-25

Peptides

Capsid protein: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwx

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A0

B
A1

C
A2

D
A3

E
A4

F
A5

G
A6

H
A7

I
A8

J
A9

K
AA

L
AB

M
AC

N
AD

O
AE

P
AF

Q
AG

R
AH

S
AI

T
AJ

U
AK

V
AL

W
AM

X
AN

Y
AO

Z
AP

0
AQ

1
AR

2
AS

3
AT

4
AU

5
AV

6
AW

7
AX

8
AY

9
AZ

a
Aa

b
Ab

c
Ac

d
Ad

e
Ae

f
Af

g
Ag

h
Ah

i
Ai

j
Aj

k
Ak

l
Al

m
Am

n
An

o
Ao

p
Ap

q
Aq

r
Ar

s
As

t
At

u
Au

v
Av

w
Aw

x
Ax

Capsid protein