SMTL ID : 8v4z.1

Crystal structure of a HLA-B*35:01-NP7 with D1 TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-4-4-4-4-mer

Ligands

4 x LEU- PRO- PHE- GLU- LYS- SER- THR- ILE- MET: LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET(Non-covalent)

LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET.1: 38 residues within 4Å: Chain A: M.5, Y.7, Y.9, R.62, N.63, I.66, F.67, T.69, N.70, T.73, E.76, S.77, N.80, L.81, Y.84, I.95, Y.99, Y.123, T.143, K.146, W.147, A.150, V.152, Q.155, L.156, Y.159, W.167, Y.171 Chain C: Y.29, G.92, G.93 Chain D: V.28, Q.48, T.95, G.96, G.97, Q.98, E.99 41 PLIP interactions: 30 interactions with chain A, 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: A:Y.7, A:F.67, A:T.73, A:E.76, A:E.76, A:L.81, A:Y.99, A:T.143, A:A.150, A:V.152, A:L.156, A:L.156, A:Y.159, A:Y.159, A:W.167, D:V.28, C:Y.29, C:Y.29 Hydrogen bonds: A:Y.7, A:T.69, A:S.77, A:N.80, A:Y.99, A:Y.99, A:T.143, A:Q.155, A:Y.159, A:Y.171, D:T.95, D:G.97, C:Y.29, C:G.93 Water bridges: A:Y.9, A:R.62, A:R.62, D:E.99, D:E.99, C:Y.29, C:Y.29 Salt bridges: A:R.62, A:K.146 LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET.2: 38 residues within 4Å: Chain E: M.5, Y.7, Y.9, R.62, N.63, I.66, F.67, T.69, N.70, T.73, E.76, S.77, N.80, L.81, Y.84, I.95, Y.99, Y.123, T.143, K.146, W.147, A.150, V.152, Q.155, L.156, Y.159, W.167, Y.171 Chain G: Y.29, G.92, G.93 Chain H: V.28, Q.48, T.95, G.96, G.97, Q.98, E.99 34 PLIP interactions: 26 interactions with chain E, 5 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: E:Y.7, E:I.66, E:F.67, E:F.67, E:T.73, E:E.76, E:E.76, E:L.81, E:Y.99, E:T.143, E:A.150, E:V.152, E:L.156, E:L.156, E:Y.159, E:W.167, G:Y.29, G:Y.29, H:V.28 Hydrogen bonds: E:T.69, E:S.77, E:N.80, E:Y.84, E:Y.99, E:Q.155, E:Y.171, E:Y.171, G:Y.29, G:Y.29, G:G.93, H:T.95, H:G.97 Salt bridges: E:R.62, E:K.146 LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET.3: 38 residues within 4Å: Chain I: M.5, Y.7, Y.9, R.62, N.63, I.66, F.67, T.69, N.70, T.73, E.76, S.77, N.80, L.81, Y.84, I.95, Y.99, Y.123, T.143, K.146, W.147, A.150, V.152, Q.155, L.156, Y.159, W.167, Y.171 Chain K: Y.29, G.92, G.93 Chain L: V.28, Q.48, T.95, G.96, G.97, Q.98, E.99 46 PLIP interactions: 35 interactions with chain I, 5 interactions with chain L, 6 interactions with chain K Hydrophobic interactions: I:Y.7, I:I.66, I:I.66, I:F.67, I:F.67, I:T.73, I:E.76, I:E.76, I:L.81, I:Y.99, I:T.143, I:A.150, I:V.152, I:L.156, I:L.156, I:Y.159, I:Y.159, I:W.167, L:V.28, K:Y.29, K:Y.29 Hydrogen bonds: I:Y.7, I:T.69, I:S.77, I:N.80, I:Y.99, I:Y.99, I:T.143, I:Q.155, I:Y.159, I:Y.171, L:T.95, L:G.97, K:Y.29, K:G.93 Water bridges: I:R.62, I:R.62, I:N.70, I:N.70, I:N.70, L:E.99, L:E.99, K:Y.29, K:Y.29 Salt bridges: I:R.62, I:K.146 LEU-PRO-PHE-GLU-LYS-SER-THR-ILE-MET.4: 37 residues within 4Å: Chain M: M.5, Y.7, Y.9, R.62, N.63, I.66, F.67, T.69, N.70, T.73, E.76, S.77, N.80, L.81, Y.84, Y.99, Y.123, T.143, K.146, W.147, A.150, V.152, Q.155, L.156, Y.159, W.167, Y.171 Chain O: Y.29, G.92, G.93 Chain P: V.28, Q.48, T.95, G.96, G.97, Q.98, E.99 36 PLIP interactions: 28 interactions with chain M, 5 interactions with chain O, 3 interactions with chain P Hydrophobic interactions: M:Y.7, M:I.66, M:F.67, M:F.67, M:T.73, M:E.76, M:E.76, M:L.81, M:Y.99, M:T.143, M:A.150, M:V.152, M:L.156, M:L.156, M:Y.159, M:W.167, O:Y.29, O:Y.29, P:V.28 Hydrogen bonds: M:Y.7, M:T.69, M:T.73, M:S.77, M:N.80, M:Y.84, M:Y.99, M:Q.155, M:Y.171, O:Y.29, O:Y.29, O:G.93, P:T.95, P:G.97 Water bridges: M:S.77 Salt bridges: M:R.62, M:K.146

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 3 residues within 4Å: Chain C: R.58, Q.78, K.80 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.78 Water bridges: C:R.58 Salt bridges: C:R.58, C:K.80 PO4.6: 2 residues within 4Å: Chain G: R.58, K.80 2 PLIP interactions: 2 interactions with chain G Salt bridges: G:R.58, G:K.80 PO4.7: 3 residues within 4Å: Chain K: R.58, Q.78, K.80 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:Q.78 Salt bridges: K:R.58, K:K.80 PO4.8: 3 residues within 4Å: Chain O: R.58, Q.78, K.80 3 PLIP interactions: 3 interactions with chain O Hydrogen bonds: O:Q.78 Salt bridges: O:R.58, O:K.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quinones-Parra, S. et al., Molecular determinants of cross-strain influenza A virus recognition by T-cell receptors. To Be Published

Release Date

2024-12-18

Peptides

MHC class I antigen: AEIM
Beta-2-microglobulin: BFJN
D1 TCR alpha chain: CGKO
D1 TCR beta chain: DHLP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
F

I
K

M
P

B
B

F
G

J
L

N
Q

C
D

G
I

K
N

O
S

D
E

H
J

L
O

P
T

MHC class I antigen

Beta-2-microglobulin

D1 TCR alpha chain

D1 TCR beta chain

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