SMTL ID : 8t7r.1

Crystal structure of human leukocyte antigen A*0101 in complex with the Fab of alloreactive antibody E07

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.84 Å

Oligo State

hetero-12-12-9-8-mer

Ligands

9 x VAL- THR- GLU- HIS- ASP- THR- LEU- LEU- TYR: peptide(Non-covalent)

VAL-THR-GLU-HIS-ASP-THR-LEU-LEU-TYR.1: 28 residues within 4Å: Chain C: M.5, Y.7, E.63, N.66, M.67, H.70, T.73, N.77, T.80, L.81, Y.84, I.95, I.97, Y.99, R.114, D.116, Y.123, T.143, K.146, W.147, A.152, Q.155, R.156, Y.159, R.163, G.167, R.170, Y.171 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:Y.7, C:T.73, C:N.77, C:L.81, C:I.95, C:T.143, C:W.147, C:W.147, C:A.152, C:Y.159, C:Y.159 Hydrogen bonds: C:Y.7, C:E.63, C:N.77, C:N.77, C:Y.84, C:Y.99, C:D.116, C:Q.155, C:Y.171 Salt bridges: C:R.156 pi-Stacking: C:Y.123 VAL-THR-GLU-HIS-ASP-THR-LEU-LEU-TYR.2: 26 residues within 4Å: Chain G: M.5, Y.7, F.9, E.63, N.66, A.69, H.70, T.73, N.77, L.81, Y.84, I.95, I.97, Y.99, D.116, Y.123, T.143, K.146, W.147, A.152, R.156, Y.159, R.163, G.167, R.170, Y.171 20 PLIP interactions: 20 interactions with chain G Hydrophobic interactions: G:F.9, G:T.73, G:N.77, G:L.81, G:I.95, G:T.143, G:W.147, G:W.147, G:A.152, G:Y.159 Hydrogen bonds: G:Y.7, G:E.63, G:A.69, G:N.77, G:N.77, G:Y.99, G:Q.155, G:Y.171 Salt bridges: G:R.156, G:R.156 VAL-THR-GLU-HIS-ASP-THR-LEU-LEU-TYR.3: 27 residues within 4Å: Chain I: D.49 Chain K: M.5, Y.7, E.63, N.66, M.67, A.69, H.70, T.73, N.77, T.80, L.81, Y.84, Y.99, R.114, D.116, Y.123, T.143, K.146, W.147, A.152, R.156, Y.159, R.163, G.167, R.170, Y.171 22 PLIP interactions: 22 interactions with chain K Hydrophobic interactions: K:Y.7, K:N.77, K:L.81, K:Y.99, K:T.143, K:W.147, K:W.147, K:Y.159 Hydrogen bonds: K:Y.7, K:E.63, K:E.63, K:N.66, K:A.69, K:N.77, K:N.77, K:Y.99, K:Y.99, K:Q.155, K:Y.159 Salt bridges: K:R.114, K:R.156, K:R.156 VAL-THR-GLU-HIS-ASP-THR-LEU-LEU-TYR.4: 23 residues within 4Å: Chain O: M.5, Y.7, F.9, E.63, N.66, M.67, H.70, T.73, N.77, T.80, L.81, Y.84, Y.99, D.116, Y.123, T.143, K.146, W.147, A.152, R.156, Y.159, R.170, Y.171 19 PLIP interactions: 19 interactions with chain O Hydrophobic interactions: O:Y.7, O:F.9, O:T.73, O:N.77, O:L.81, O:T.143, O:W.147, O:Y.159, O:Y.159 Hydrogen bonds: O:E.63, O:A.69, O:N.77, O:N.77, O:Y.99, O:Y.99, O:Y.159, O:Y.171 Salt bridges: O:R.156 pi-Cation interactions: O:R.163 VAL-THR-GLU-HIS-ASP-THR-LEU-LEU-TYR.5: 27 residues within 4Å: Chain S: M.5, Y.7, F.9, E.63, N.66, M.67, A.69, H.70, T.73, N.77, T.80, L.81, Y.84, I.95, Y.99, D.116, Y.123, T.143, K.146, W.147, A.152, Q.155, R.156, Y.159, R.163, G.167, Y.171 29 PLIP interactions: 29 interactions with chain S Hydrophobic interactions: S:Y.7, S:F.9, S:H.70, S:T.73, S:N.77, S:L.81, S:I.95, S:Y.123, S:T.143, S:W.147, S:W.147 Hydrogen bonds: S:Y.7, S:E.63, S:E.63, S:A.69, S:T.73, S:N.77, S:N.77, S:Y.84, S:Y.99, S:Y.99, S:D.116, S:D.116, S:Q.155, S:R.156, S:Y.171, S:Y.171 Salt bridges: S:R.156, S:R.156 VAL-THR-GLU-HIS-ASP-THR-LEU-LEU-TYR.6: 26 residues within 4Å: Chain W: M.5, Y.7, F.9, E.63, N.66, M.67, A.69, H.70, T.73, N.77, T.80, L.81, Y.84, I.95, I.97, Y.99, D.116, T.143, K.146, W.147, A.152, R.156, Y.159, R.163, G.167, Y.171 22 PLIP interactions: 22 interactions with chain W Hydrophobic interactions: W:F.9, W:T.73, W:N.77, W:L.81, W:I.95, W:Y.99, W:T.143, W:W.147, W:W.147, W:A.152, W:Y.159 Hydrogen bonds: W:Y.7, W:Y.7, W:E.63, W:T.73, W:T.73, W:N.77, W:N.77, W:Y.99, W:D.116, W:Y.171 Salt bridges: W:R.156 VAL-THR-GLU-HIS-ASP-THR-LEU-LEU-TYR.7: 27 residues within 4Å: Chain 0: M.5, Y.7, E.63, N.66, M.67, A.69, H.70, T.73, D.74, A.76, N.77, L.81, Y.84, I.95, Y.99, D.116, T.143, K.146, W.147, V.150, Q.155, R.156, Y.159, R.163, G.167, R.170, Y.171 29 PLIP interactions: 29 interactions with chain 0 Hydrophobic interactions: 0:Y.7, 0:T.73, 0:A.76, 0:N.77, 0:L.81, 0:I.95, 0:W.147, 0:V.150, 0:Y.159, 0:Y.159, 0:R.163 Hydrogen bonds: 0:E.63, 0:E.63, 0:N.66, 0:A.69, 0:D.74, 0:N.77, 0:N.77, 0:Y.84, 0:Y.99, 0:Y.99, 0:D.116, 0:Q.155, 0:R.156, 0:Y.159, 0:R.163, 0:Y.171 Salt bridges: 0:R.156, 0:R.156 VAL-THR-GLU-HIS-ASP-THR-LEU-LEU-TYR.8: 25 residues within 4Å: Chain 4: M.5, Y.7, Q.62, E.63, N.66, M.67, H.70, T.73, N.77, L.81, Y.84, I.97, Y.99, D.116, Y.123, T.143, K.146, W.147, Q.155, R.156, Y.159, R.163, G.167, R.170, Y.171 27 PLIP interactions: 27 interactions with chain 4 Hydrophobic interactions: 4:E.63, 4:N.66, 4:T.73, 4:N.77, 4:L.81, 4:T.143, 4:W.147, 4:Y.159, 4:Y.159 Hydrogen bonds: 4:Y.7, 4:Y.7, 4:E.63, 4:A.69, 4:T.73, 4:N.77, 4:N.77, 4:Y.84, 4:Y.99, 4:Y.99, 4:D.116, 4:K.146, 4:Q.155, 4:R.156, 4:Y.171 Salt bridges: 4:R.156, 4:R.156 pi-Stacking: 4:Y.123 VAL-THR-GLU-HIS-ASP-THR-LEU-LEU-TYR.9: 23 residues within 4Å: Chain 8: Y.7, Y.59, E.63, N.66, A.69, H.70, T.73, N.77, T.80, Y.84, Y.99, R.114, D.116, Y.123, T.143, K.146, W.147, Q.155, R.156, Y.159, R.163, G.167, Y.171 21 PLIP interactions: 21 interactions with chain 8 Hydrophobic interactions: 8:E.63, 8:N.66, 8:N.77, 8:Y.123, 8:W.147, 8:Y.159 Hydrogen bonds: 8:Y.59, 8:E.63, 8:N.66, 8:T.73, 8:N.77, 8:N.77, 8:Y.99, 8:Q.155, 8:R.156, 8:Y.159, 8:Y.171, 8:Y.171 Salt bridges: 8:R.114, 8:R.156, 8:R.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Killian Jr, J.T. et al., B cell and antibody targeting of transplant alloantigen epitopes is supported by both self and allo-recognition. To Be Published

Release Date

2024-12-25

Peptides

Light chain from antibody JTK191b E07: AEIMQUY269bd
Fab heavy chain from antibody JTK191b E07: BFJNRVZ37ace
MHC class I antigen (Fragment): CGKOSW048
Beta-2-microglobulin: DHLPTX15

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

M
M

Q
Q

U
U

Y
Y

2
c

6
g

9
k

b
o

d
s

B
B

F
F

J
J

N
N

R
R

V
V

Z
Z

3
d

7
h

a
l

c
p

e
t

C
C

G
G

K
K

O
O

S
S

W
W

0
a

4
e

8
i

D
D

H
H

L
L

P
P

T
T

X
X

1
b

5
f

Light chain from antibody JTK191b E07

Fab heavy chain from antibody JTK191b E07

MHC class I antigen (Fragment)

Beta-2-microglobulin

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