SMTL ID : 7bbg.1

CRYSTAL STRUCTURE OF HLA-A2-WT1-RMF AND FAB 11D06

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ARG- MET- PHE- PRO- ASN- ALA- PRO- TYR- LEU: Wilms tumor 1 (WT1) derived peptide(Non-covalent)

ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU.1: 35 residues within 4Å: Chain A: M.6, Y.8, F.10, M.46, Y.60, E.64, K.67, H.71, T.74, V.77, D.78, T.81, L.82, Y.85, R.98, Y.100, Y.117, Y.124, T.144, K.147, W.148, V.153, Q.156, L.157, Y.160, W.168, Y.172 Chain C: S.31, I.100, E.101, W.104 Chain D: S.28, S.30, W.32, E.92 33 PLIP interactions: 29 interactions with chain A, 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:T.74, A:V.77, A:D.78, A:L.82, A:Y.100, A:Y.124, A:T.144, A:W.148, A:V.153, A:V.153, A:Q.156, A:L.157, A:Y.160, A:Y.160, A:W.168, C:W.104 Hydrogen bonds: A:Y.8, A:Y.60, A:E.64, A:K.67, A:D.78, A:R.98, A:R.98, A:Y.100, A:Y.100, A:K.147, A:Y.160, A:Y.172, D:E.92 Water bridges: A:W.168, C:S.31 Salt bridges: A:E.64, C:E.101

5 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: D.38, A.41, S.43, Q.44, R.45 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.41, A:A.41, A:Q.44, A:R.45 Water bridges: A:D.38 NA.3: 4 residues within 4Å: Chain A: S.5, R.7, Y.28, D.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.5, A:D.30 NA.4: 6 residues within 4Å: Chain A: Y.8, F.34, V.35, M.46, Y.60, E.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.60, A:E.64 NA.5: 6 residues within 4Å: Chain C: F.173, P.174, L.185, S.186 Chain D: S.161, S.175 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.186, D:S.161, D:S.175, D:S.175 NA.6: 4 residues within 4Å: Chain C: R.67, T.69, E.82, S.84 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.67, C:T.69, C:S.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Augsberger, C. et al., Targeting intracellular WT1 in AML with a novel RMF-peptide-MHC-specific T-cell bispecific antibody. Blood (2021)

Release Date

2021-10-27

Peptides

MHC class I antigen: A
Beta-2-microglobulin: B
Heavy chain of Fab fragment 11D06: C
Light chain of Fab fragment 11D06: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

MHC class I antigen

Beta-2-microglobulin

Heavy chain of Fab fragment 11D06

Light chain of Fab fragment 11D06

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