SMTL ID : 5dk3.1

Crystal Structure of Pembrolizumab, a full length IgG4 antibody

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-MAN-NAG.1: 11 residues within 4Å: Chain B: S.141, F.241, F.243, P.247, T.260, V.264, D.265, Q.295, N.297, T.299, R.301 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-NAG-MAN-FUC.2: 13 residues within 4Å: Chain B: Q.274, N.276, Y.278, S.324 Chain D: F.241, F.243, T.260, V.264, D.265, Q.295, N.297, T.299, R.301 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.276, B:N.276, B:Y.278, B:S.324

3 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.3: 8 residues within 4Å: Chain B: I.377, A.378, V.379, Y.391, K.392, T.393, P.395, P.396 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.393, B:V.379, B:V.379 Water bridges: B:V.379, B:I.377, B:T.393, B:T.393, B:T.393 GLC-FRU.4: 12 residues within 4Å: Chain B: K.360, Q.362, N.390, R.409, T.411 Chain D: R.344, Q.347, K.370, D.399, S.400, D.401 Ligands: SO4.8 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:R.344, D:Q.347, D:Q.347, D:D.401, D:D.401, B:Q.362, B:Q.362, B:N.390, B:R.409, B:R.409, D:K.370, D:D.399, D:D.401 Water bridges: D:S.403, D:S.403, D:D.401, D:S.403 GLC-FRU.5: 7 residues within 4Å: Chain D: F.88, T.91, S.119, L.177, Q.178, S.179, G.181 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.91, D:T.91, D:S.119

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

SO4.6: 6 residues within 4Å: Chain A: K.43, R.49, P.63, R.65, F.66, E.85 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.43 Salt bridges: A:K.43, A:R.49, A:R.65 SO4.7: 4 residues within 4Å: Chain B: Y.27, T.28, N.31, Y.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:N.31 SO4.8: 4 residues within 4Å: Chain B: K.360, N.361, Q.362 Ligands: GLC-FRU.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.361, B:Q.362, B:Q.362 Salt bridges: B:K.360 SO4.9: 3 residues within 4Å: Chain A: E.169, D.171 Chain B: H.171 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.171, A:D.171 Water bridges: A:S.172, B:V.170, B:T.172 Salt bridges: B:H.171 SO4.10: 3 residues within 4Å: Chain B: W.313, K.338, A.339 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.339 Salt bridges: B:K.338

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scapin, G. et al., Structure of full-length human anti-PD1 therapeutic IgG4 antibody pembrolizumab. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-11-18

Peptides

Light Chain: AC
Heavy Chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
F

B
B

D
G

Light Chain

Heavy Chain

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