SMTL ID : 9djw.1

X-ray crystal structure of TNFa-VNAR D1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.31 Å

Oligo State

hetero-30-30-mer

Ligands

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: A.2 Chain w: R.31, A.32 Ligand excluded by PLIP GOL.2: 2 residues within 4Å: Chain B: R.3, V.97 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain F: A.31, T.32, S.33, S.62, K.65 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain 2: K.89 Chain L: R.39, R.55, Y.56 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain R: A.31, T.32, S.33, S.62, K.65 Ligand excluded by PLIP GOL.7: 2 residues within 4Å: Chain X: R.39, Y.56 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain 3: R.39, R.55, Y.56 Chain w: K.89 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain 4: A.2, R.3, V.97 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain 8: R.31 Chain a: R.3, D.96, V.97 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain 9: A.31, T.32, S.33, K.65 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain 9: R.39, R.55, Y.56 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain 8: V.90 Chain 9: R.3, V.97 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain c: A.32 Chain f: A.2, R.3, Y.98 Ligand excluded by PLIP GOL.17: 2 residues within 4Å: Chain l: R.55, Y.56 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain r: R.39, R.55, Y.56 Ligand excluded by PLIP GOL.20: 1 residues within 4Å: Chain r: R.3 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain x: A.2, R.3, V.97 Ligand excluded by PLIP

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

SO4.6: 4 residues within 4Å: Chain X: A.31, T.32, S.33, K.65 3 PLIP interactions: 3 interactions with chain X Hydrogen bonds: X:T.32, X:S.33 Salt bridges: X:K.65 SO4.15: 3 residues within 4Å: Chain f: A.31, T.32, S.33 3 PLIP interactions: 3 interactions with chain f Hydrogen bonds: f:T.32, f:S.33, f:S.33 SO4.18: 4 residues within 4Å: Chain r: A.31, T.32, S.33, K.65 3 PLIP interactions: 3 interactions with chain r Hydrogen bonds: r:T.32, r:S.33 Salt bridges: r:K.65

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 1 residues within 4Å: Chain 0: K.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ubah, O.C. et al., The structural basis for the selective antagonism of soluble TNF-alpha by multivalent, bi-paratopic variable new antigen receptor (VNAR). To Be Published

Release Date

2025-09-10

Peptides

Antigen receptor: ABFGHLMNRSTXYZ3459abfghlmnrstx
Tumor necrosis factor: CDEIJKOPQUVW012678cdeijkopquvw

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

F
5

G
6

H
7

L
D

M
E

N
F

R
J

S
K

T
L

X
P

Y
Q

Z
R

3
V

4
W

5
X

9
b

a
c

b
d

f
h

g
i

h
j

l
n

m
o

n
p

r
t

s
u

t
v

x
z

C
2

D
3

E
4

I
A

J
B

K
C

O
G

P
H

Q
I

U
M

V
N

W
O

0
S

1
T

2
U

6
Y

7
Z

8
a

c
e

d
f

e
g

i
k

j
l

k
m

o
q

p
r

q
s

u
w

v
x

w
y

Antigen receptor

Tumor necrosis factor