SMTL ID : 6id4.2 (1 other biounit)

Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ALA- ILE- PHE- GLN- SER- SER- MET- THR- LYS: peptide(Non-covalent)

ALA-ILE-PHE-GLN-SER-SER-MET-THR-LYS.1: 29 residues within 4Å: Chain C: M.6, Y.8, Y.10, M.46, Q.63, E.64, N.67, V.68, Q.71, T.74, V.77, D.78, T.81, Y.85, Y.100, R.115, D.117, Y.124, T.144, K.147, W.148, A.151, A.153, Q.156, Q.157, Y.160, R.164, W.168, Y.172 33 PLIP interactions: 33 interactions with chain C Hydrophobic interactions: C:Y.8, C:N.67, C:V.77, C:Y.100, C:Y.124, C:T.144, C:W.148, C:Y.160, C:Y.160, C:Y.160, C:W.168 Hydrogen bonds: C:Q.63, C:E.64, C:N.67, C:Q.71, C:Q.71, C:D.78, C:Y.85, C:Y.100, C:Y.100, C:R.115, C:R.115, C:D.117, C:T.144, C:Q.156, C:Y.160, C:R.164, C:R.164, C:Y.172 Water bridges: C:T.74, C:D.78, C:D.78 Salt bridges: C:K.147

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain B: N.34, Y.36, I.98, W.99, W.104 Chain C: P.16, D.91 Ligands: PEG.3 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.34, B:N.34, B:N.34, B:Y.36, B:W.99, C:P.16, C:D.91 GOL.4: 6 residues within 4Å: Chain C: R.7, F.9, Y.28, D.30, D.31 Chain D: Y.64 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.64, C:R.7, C:D.31, C:D.31

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 8 residues within 4Å: Chain A: I.103 Chain C: R.15, P.16, R.18, D.91, G.92, S.93 Ligands: GOL.2 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.18, C:S.93 Water bridges: B:N.34, B:D.57, B:D.57 PEG.5: 7 residues within 4Å: Chain C: R.7, M.99, R.112, Y.114, Q.116 Chain D: K.59 Ligands: PEG.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.7, C:R.112 PEG.6: 7 residues within 4Å: Chain C: F.9, M.99 Chain D: F.57, S.58, K.59, W.61 Ligands: PEG.5 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.59, D:K.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, Y. et al., Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01. Nat Commun (2019)

Release Date

2019-02-06

Peptides

Heavy chain: A
Light chain: B
MHC class I antigen: C
Beta-2-microglobulin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

Heavy chain

Light chain

MHC class I antigen

Beta-2-microglobulin

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