SMTL ID : 2gsy.1

The 2.6A structure of Infectious Bursal Virus Derived T=1 Particles

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-60-mer

Ligands

33 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain 5: D.31, D.174 Chain A: D.31, D.174 Chain E: D.31, D.174 Ligands: CA.18 6 PLIP interactions: 2 interactions with chain 5, 2 interactions with chain A, 2 interactions with chain E Metal complexes: 5:D.31, 5:D.174, A:D.31, A:D.174, E:D.31, E:D.174 CA.2: 7 residues within 4Å: Chain 3: D.31, D.174 Chain B: D.31, D.174 Chain W: D.31, D.174 Ligands: CA.14 6 PLIP interactions: 2 interactions with chain W, 2 interactions with chain 3, 2 interactions with chain B Metal complexes: W:D.31, W:D.174, 3:D.31, 3:D.174, B:D.31, B:D.174 CA.3: 7 residues within 4Å: Chain C: D.31, D.174 Chain J: D.31, D.174 Ligands: CA.24 Chain f: D.31, D.174 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain J, 2 interactions with chain f Metal complexes: C:D.31, C:D.174, J:D.31, J:D.174, f:D.31, f:D.174 CA.4: 8 residues within 4Å: Chain D: D.31, D.174 Chain X: D.31, D.174 Ligands: CA.15, CA.26 Chain h: D.31, D.174 5 PLIP interactions: 2 interactions with chain h, 1 interactions with chain X, 2 interactions with chain D Metal complexes: h:D.31, h:D.174, X:D.31, D:D.31, D:D.174 CA.5: 6 residues within 4Å: Chain F: D.31, D.174 Chain I: D.31, D.174 Chain K: D.31, D.174 6 PLIP interactions: 2 interactions with chain I, 2 interactions with chain F, 2 interactions with chain K Metal complexes: I:D.31, I:D.174, F:D.31, F:D.174, K:D.31, K:D.174 CA.6: 6 residues within 4Å: Chain G: D.31, D.174 Chain H: D.31, D.174 Chain N: D.31, D.174 6 PLIP interactions: 2 interactions with chain N, 2 interactions with chain G, 2 interactions with chain H Metal complexes: N:D.31, N:D.174, G:D.31, G:D.174, H:D.31, H:D.174 CA.7: 7 residues within 4Å: Chain L: D.31, D.174 Ligands: CA.23 Chain e: D.31, D.174 Chain i: D.31, D.174 6 PLIP interactions: 2 interactions with chain e, 2 interactions with chain L, 2 interactions with chain i Metal complexes: e:D.31, e:D.174, L:D.31, L:D.174, i:D.31, i:D.174 CA.8: 7 residues within 4Å: Chain M: D.31, D.174 Chain R: D.31, D.174 Ligands: CA.32 Chain w: D.31, D.174 6 PLIP interactions: 2 interactions with chain w, 2 interactions with chain M, 2 interactions with chain R Metal complexes: w:D.31, w:D.174, M:D.31, M:D.174, R:D.31, R:D.174 CA.9: 6 residues within 4Å: Chain O: D.31, D.174 Chain P: D.31, D.174 Chain Q: D.31, D.174 6 PLIP interactions: 2 interactions with chain P, 2 interactions with chain O, 2 interactions with chain Q Metal complexes: P:D.31, P:D.174, O:D.31, O:D.174, Q:D.31, Q:D.174 CA.10: 7 residues within 4Å: Chain 6: D.31, D.174 Chain S: D.31, D.174 Ligands: CA.19 Chain b: D.31, D.174 6 PLIP interactions: 2 interactions with chain b, 2 interactions with chain 6, 2 interactions with chain S Metal complexes: b:D.31, b:D.174, 6:D.31, 6:D.174, S:D.31, S:D.174 CA.11: 8 residues within 4Å: Chain T: D.31, D.174 Ligands: CA.22, CA.33 Chain d: D.31, D.174 Chain x: D.31, D.174 6 PLIP interactions: 2 interactions with chain x, 2 interactions with chain d, 2 interactions with chain T Metal complexes: x:D.31, x:D.174, d:D.31, d:D.174, T:D.31, T:D.174 CA.12: 7 residues within 4Å: Chain U: D.31, D.174 Chain Y: D.31, D.174 Ligands: CA.29 Chain p: D.31, D.174 6 PLIP interactions: 2 interactions with chain U, 2 interactions with chain p, 2 interactions with chain Y Metal complexes: U:D.31, U:D.174, p:D.31, p:D.174, Y:D.31, Y:D.174 CA.13: 7 residues within 4Å: Chain V: D.31, D.174 Ligands: CA.25 Chain g: D.31, D.174 Chain n: D.31, D.174 6 PLIP interactions: 2 interactions with chain g, 2 interactions with chain V, 2 interactions with chain n Metal complexes: g:D.31, g:D.174, V:D.31, V:D.174, n:D.31, n:D.174 CA.14: 7 residues within 4Å: Chain 3: D.31, D.174 Chain B: D.31, D.174 Chain W: D.31, D.174 Ligands: CA.2 6 PLIP interactions: 2 interactions with chain W, 2 interactions with chain 3, 2 interactions with chain B Metal complexes: W:D.31, W:D.174, 3:D.31, 3:D.174, B:D.31, B:D.174 CA.15: 8 residues within 4Å: Chain D: D.31, D.174 Chain X: D.31, D.174 Ligands: CA.4, CA.26 Chain h: D.31, D.174 5 PLIP interactions: 2 interactions with chain X, 1 interactions with chain h, 2 interactions with chain D Metal complexes: X:D.31, X:D.174, h:D.31, D:D.31, D:D.174 CA.16: 6 residues within 4Å: Chain 2: D.31, D.174 Chain 4: D.31, D.174 Chain Z: D.31, D.174 6 PLIP interactions: 2 interactions with chain 4, 2 interactions with chain 2, 2 interactions with chain Z Metal complexes: 4:D.31, 4:D.174, 2:D.31, 2:D.174, Z:D.31, Z:D.174 CA.17: 6 residues within 4Å: Chain 0: D.31, D.174 Chain 1: D.31, D.174 Chain 7: D.31, D.174 6 PLIP interactions: 2 interactions with chain 7, 2 interactions with chain 1, 2 interactions with chain 0 Metal complexes: 7:D.31, 7:D.174, 1:D.31, 1:D.174, 0:D.31, 0:D.174 CA.18: 7 residues within 4Å: Chain 5: D.31, D.174 Chain A: D.31, D.174 Chain E: D.31, D.174 Ligands: CA.1 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E, 2 interactions with chain 5 Metal complexes: A:D.31, A:D.174, E:D.31, E:D.174, 5:D.31, 5:D.174 CA.19: 7 residues within 4Å: Chain 6: D.31, D.174 Chain S: D.31, D.174 Ligands: CA.10 Chain b: D.31, D.174 6 PLIP interactions: 2 interactions with chain b, 2 interactions with chain S, 2 interactions with chain 6 Metal complexes: b:D.31, b:D.174, S:D.31, S:D.174, 6:D.31, 6:D.174 CA.20: 6 residues within 4Å: Chain 8: D.31, D.174 Chain 9: D.31, D.174 Chain a: D.31, D.174 6 PLIP interactions: 2 interactions with chain 8, 2 interactions with chain a, 2 interactions with chain 9 Metal complexes: 8:D.31, 8:D.174, a:D.31, a:D.174, 9:D.31, 9:D.174 CA.21: 7 residues within 4Å: Ligands: CA.30 Chain c: D.31, D.174 Chain q: D.31, D.174 Chain v: D.31, D.174 6 PLIP interactions: 2 interactions with chain c, 2 interactions with chain v, 2 interactions with chain q Metal complexes: c:D.31, c:D.174, v:D.31, v:D.174, q:D.31, q:D.174 CA.22: 8 residues within 4Å: Chain T: D.31, D.174 Ligands: CA.11, CA.33 Chain d: D.31, D.174 Chain x: D.31, D.174 6 PLIP interactions: 2 interactions with chain T, 2 interactions with chain x, 2 interactions with chain d Metal complexes: T:D.31, T:D.174, x:D.31, x:D.174, d:D.31, d:D.174 CA.23: 7 residues within 4Å: Chain L: D.31, D.174 Ligands: CA.7 Chain e: D.31, D.174 Chain i: D.31, D.174 6 PLIP interactions: 2 interactions with chain e, 2 interactions with chain L, 2 interactions with chain i Metal complexes: e:D.31, e:D.174, L:D.31, L:D.174, i:D.31, i:D.174 CA.24: 7 residues within 4Å: Chain C: D.31, D.174 Chain J: D.31, D.174 Ligands: CA.3 Chain f: D.31, D.174 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain J, 2 interactions with chain f Metal complexes: C:D.31, C:D.174, J:D.31, J:D.174, f:D.31, f:D.174 CA.25: 7 residues within 4Å: Chain V: D.31, D.174 Ligands: CA.13 Chain g: D.31, D.174 Chain n: D.31, D.174 6 PLIP interactions: 2 interactions with chain n, 2 interactions with chain V, 2 interactions with chain g Metal complexes: n:D.31, n:D.174, V:D.31, V:D.174, g:D.31, g:D.174 CA.26: 8 residues within 4Å: Chain D: D.31, D.174 Chain X: D.31, D.174 Ligands: CA.4, CA.15 Chain h: D.31, D.174 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain X, 2 interactions with chain h Metal complexes: D:D.31, X:D.31, X:D.174, h:D.31, h:D.174 CA.27: 6 residues within 4Å: Chain j: D.31, D.174 Chain m: D.31, D.174 Chain o: D.31, D.174 6 PLIP interactions: 2 interactions with chain j, 2 interactions with chain m, 2 interactions with chain o Metal complexes: j:D.31, j:D.174, m:D.31, m:D.174, o:D.31, o:D.174 CA.28: 6 residues within 4Å: Chain k: D.31, D.174 Chain l: D.31, D.174 Chain r: D.31, D.174 6 PLIP interactions: 2 interactions with chain r, 2 interactions with chain l, 2 interactions with chain k Metal complexes: r:D.31, r:D.174, l:D.31, l:D.174, k:D.31, k:D.174 CA.29: 7 residues within 4Å: Chain U: D.31, D.174 Chain Y: D.31, D.174 Ligands: CA.12 Chain p: D.31, D.174 6 PLIP interactions: 2 interactions with chain p, 2 interactions with chain U, 2 interactions with chain Y Metal complexes: p:D.31, p:D.174, U:D.31, U:D.174, Y:D.31, Y:D.174 CA.30: 7 residues within 4Å: Ligands: CA.21 Chain c: D.31, D.174 Chain q: D.31, D.174 Chain v: D.31, D.174 6 PLIP interactions: 2 interactions with chain c, 2 interactions with chain v, 2 interactions with chain q Metal complexes: c:D.31, c:D.174, v:D.31, v:D.174, q:D.31, q:D.174 CA.31: 6 residues within 4Å: Chain s: D.31, D.174 Chain t: D.31, D.174 Chain u: D.31, D.174 6 PLIP interactions: 2 interactions with chain u, 2 interactions with chain t, 2 interactions with chain s Metal complexes: u:D.31, u:D.174, t:D.31, t:D.174, s:D.31, s:D.174 CA.32: 7 residues within 4Å: Chain M: D.31, D.174 Chain R: D.31, D.174 Ligands: CA.8 Chain w: D.31, D.174 6 PLIP interactions: 2 interactions with chain w, 2 interactions with chain M, 2 interactions with chain R Metal complexes: w:D.31, w:D.174, M:D.31, M:D.174, R:D.31, R:D.174 CA.33: 8 residues within 4Å: Chain T: D.31, D.174 Ligands: CA.11, CA.22 Chain d: D.31, D.174 Chain x: D.31, D.174 6 PLIP interactions: 2 interactions with chain d, 2 interactions with chain x, 2 interactions with chain T Metal complexes: d:D.31, d:D.174, x:D.31, x:D.174, T:D.31, T:D.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garriga, D. et al., The 2.6-angstrom structure of infectious bursal disease virus-derived t=1 particles reveals new stabilizing elements of the virus capsid. J.Virol. (2006)

Release Date

2006-07-18

Peptides

polyprotein: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwx

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

S
S

T
T

U
A

V
B

W
C

X
D

Y
E

Z
F

0
G

1
H

2
I

3
J

4
K

5
L

6
M

7
N

8
O

9
P

a
Q

b
R

c
S

d
T

e
A

f
B

g
C

h
D

i
E

j
F

k
G

l
H

m
I

n
J

o
K

p
L

q
M

r
N

s
O

t
P

u
Q

v
R

w
S

x
T

polyprotein