SMTL ID : 9bf9.1

Human LAG-3-HLA-DR1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 7 residues within 4Å: Chain D: T.152, N.168, S.170, R.173, F.205 Chain H: R.176, E.203 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:E.203 NAG-NAG-BMA-MAN-MAN.7: 7 residues within 4Å: Chain D: R.176, E.203 Chain H: T.152, N.168, S.170, R.173, F.205 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.203

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

SO4.2: 2 residues within 4Å: Chain A: V.128, T.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.130 SO4.5: 1 residues within 4Å: Chain D: R.194 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.194 SO4.6: 4 residues within 4Å: Chain D: Q.97, P.98, R.99, R.120 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.120 SO4.8: 2 residues within 4Å: Chain E: V.128, T.130 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.130 SO4.11: 1 residues within 4Å: Chain H: R.194 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:R.194 SO4.12: 4 residues within 4Å: Chain H: Q.97, P.98, R.99, R.120 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:R.120

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain D: N.230 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain H: N.230 No protein-ligand interaction detected (PLIP)

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

PEG.4: 1 residues within 4Å: Chain D: Q.188 No protein-ligand interaction detected (PLIP) PEG.10: 1 residues within 4Å: Chain H: Q.188 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petersen, J. et al., Crystal structure of the human LAG-3-HLA-DR1-peptide complex. Sci Immunol (2024)

Release Date

2024-12-25

Peptides

HLA class II histocompatibility antigen, DR alpha chain: AE
HLA class II histocompatibility antigen DR beta chain: BF
Membrane protein: CG
Lymphocyte activation gene 3 protein: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

B
B

F
B

C
G

G
G

D
D

H
D

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen DR beta chain

Membrane protein

Lymphocyte activation gene 3 protein

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