SMTL ID : 4y4y.1

T=1 capsid structure of SeMV Ndel65CP fused with B-domain of S. aureus protein SpA at the N-terminus (C2 crystal form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-60-mer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 10 residues within 4Å: Chain A: S.147, S.148 Chain B: S.147, S.148 Chain C: S.147, S.148 Chain D: S.147, S.148 Chain E: S.147, S.148 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: E:S.147, E:S.147, A:S.147, D:S.147 SO4.2: 10 residues within 4Å: Chain 0: S.147, S.148 Chain H: S.147, S.148 Chain I: S.147, S.148 Chain J: S.147, S.148 Chain Z: S.147, S.148 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain H Hydrogen bonds: J:S.147, J:S.148, H:S.147, H:S.147 SO4.3: 10 residues within 4Å: Chain 1: S.147, S.148 Chain K: S.147, S.148 Chain L: S.147, S.148 Chain r: S.147, S.148 Chain s: S.147, S.148 6 PLIP interactions: 3 interactions with chain L, 1 interactions with chain s, 2 interactions with chain r Hydrogen bonds: L:S.147, L:S.148, L:S.148, s:S.147, r:S.147, r:S.147 SO4.4: 10 residues within 4Å: Chain 2: S.147, S.148 Chain M: S.147, S.148 Chain N: S.147, S.148 Chain n: S.147, S.148 Chain o: S.147, S.148 6 PLIP interactions: 2 interactions with chain n, 1 interactions with chain o, 1 interactions with chain M, 2 interactions with chain 2 Hydrogen bonds: n:S.147, n:S.148, o:S.147, M:S.147, 2:S.147, 2:S.147 SO4.5: 10 residues within 4Å: Chain 3: S.147, S.148 Chain O: S.147, S.148 Chain P: S.147, S.148 Chain Q: S.147, S.148 Chain S: S.147, S.148 5 PLIP interactions: 1 interactions with chain O, 1 interactions with chain S, 1 interactions with chain P, 2 interactions with chain 3 Hydrogen bonds: O:S.147, S:S.147, P:S.147, 3:S.147, 3:S.147 SO4.6: 10 residues within 4Å: Chain F: S.147, S.148 Chain G: S.147, S.148 Chain R: S.147, S.148 Chain V: S.147, S.148 Chain W: S.147, S.148 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain V Hydrogen bonds: G:S.147, V:S.147 SO4.7: 10 residues within 4Å: Chain 4: S.147, S.148 Chain 5: S.147, S.148 Chain 6: S.147, S.148 Chain 7: S.147, S.148 Chain 8: S.147, S.148 4 PLIP interactions: 1 interactions with chain 4, 2 interactions with chain 8, 1 interactions with chain 7 Hydrogen bonds: 4:S.147, 8:S.147, 8:S.147, 7:S.147 SO4.8: 10 residues within 4Å: Chain b: S.147, S.148 Chain c: S.147, S.148 Chain d: S.147, S.148 Chain t: S.147, S.148 Chain u: S.147, S.148 4 PLIP interactions: 2 interactions with chain b, 2 interactions with chain d Hydrogen bonds: b:S.147, b:S.147, d:S.147, d:S.148 SO4.9: 10 residues within 4Å: Chain X: S.147, S.148 Chain Y: S.147, S.148 Chain e: S.147, S.148 Chain f: S.147, S.148 Chain v: S.147, S.148 6 PLIP interactions: 2 interactions with chain X, 3 interactions with chain f, 1 interactions with chain Y Hydrogen bonds: X:S.147, X:S.147, f:S.147, f:S.148, f:S.148, Y:S.147 SO4.10: 10 residues within 4Å: Chain T: S.147, S.148 Chain U: S.147, S.148 Chain g: S.147, S.148 Chain h: S.147, S.148 Chain w: S.147, S.148 6 PLIP interactions: 1 interactions with chain U, 2 interactions with chain w, 1 interactions with chain g, 2 interactions with chain T Hydrogen bonds: U:S.147, w:S.147, w:S.147, g:S.147, T:S.147, T:S.148 SO4.11: 10 residues within 4Å: Chain i: S.147, S.148 Chain j: S.147, S.148 Chain k: S.147, S.148 Chain m: S.147, S.148 Chain x: S.147, S.148 5 PLIP interactions: 1 interactions with chain i, 1 interactions with chain m, 2 interactions with chain x, 1 interactions with chain j Hydrogen bonds: i:S.147, m:S.147, x:S.147, x:S.147, j:S.147 SO4.12: 10 residues within 4Å: Chain 9: S.147, S.148 Chain a: S.147, S.148 Chain l: S.147, S.148 Chain p: S.147, S.148 Chain q: S.147, S.148 2 PLIP interactions: 1 interactions with chain a, 1 interactions with chain p Hydrogen bonds: a:S.147, p:S.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gulati, A. et al., Structural studies on chimeric Sesbania mosaic virus coat protein: Revisiting SeMV assembly. Virology (2015)

Release Date

2016-01-20

Peptides

Immunoglobulin G-binding protein A,Coat protein: 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
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

1
b

2
c

3
d

4
A

5
B

6
C

7
D

8
E

9
F

a
G

b
H

c
I

d
J

e
K

f
L

g
M

h
N

i
O

j
P

k
Q

l
R

m
S

n
T

o
U

p
V

q
W

r
X

s
Y

t
Z

u
a

v
b

w
c

x
d

Immunoglobulin G-binding protein A,Coat protein

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