SMTL ID : 5m5e.1

Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-FUC.1: 5 residues within 4Å: Chain A: H.36, W.38, R.43, N.45, R.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.36, A:R.81 Water bridges: A:R.81 Hydrophobic interactions: A:W.38 NAG-NAG-FUC.2: 10 residues within 4Å: Chain A: F.11, N.17, S.19, N.61, R.105, L.106, M.107, A.108, Q.130, P.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.19, A:R.105, A:L.106, A:A.108, A:N.61

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 5 residues within 4Å: Chain A: V.115, N.123, W.166 Chain B: T.176 Ligands: CYS.8 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.4: 5 residues within 4Å: Chain B: P.60, N.62, F.85, E.88, I.89 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.89

1 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.5: 4 residues within 4Å: Chain A: R.183, K.185, T.193, W.194 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.183, A:R.183, A:T.193, A:T.193, A:W.194, A:W.194

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

SO4.6: 4 residues within 4Å: Chain A: R.42, R.43, W.44 Chain C: S.106 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.43, C:S.106 Water bridges: A:R.42, A:W.44 Salt bridges: A:R.42 SO4.7: 5 residues within 4Å: Chain A: G.65, A.66, S.69, K.71 Chain C: D.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.66, A:S.69 Salt bridges: A:K.71 SO4.11: 3 residues within 4Å: Chain B: E.136, N.137, H.220 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.137, B:N.137 Water bridges: B:L.138, B:L.138, B:H.220, B:H.220 Salt bridges: B:H.220 SO4.12: 4 residues within 4Å: Chain C: K.68, E.71, K.73, H.74 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:K.68, C:K.73, C:H.74

1 x CYS: CYSTEINE(Non-covalent)

CYS.8: 6 residues within 4Å: Chain A: H.116, E.118, R.121, N.123, C.168 Ligands: NAG-NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.118, A:N.123

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

NAG.9: 5 residues within 4Å: Chain B: F.43, Y.47, N.49, L.84, Q.94 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.43 Hydrogen bonds: B:Y.47, B:Q.94 Water bridges: B:N.49 NAG.10: 5 residues within 4Å: Chain B: E.136, N.137, N.153, N.154, R.155 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.153, B:R.155 Hydrogen bonds: B:E.136, B:E.136, B:N.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klein, C. et al., Cergutuzumab amunaleukin (CEA-IL2v), a CEA-targeted IL-2 variant-based immunocytokine for combination cancer immunotherapy: Overcoming limitations of aldesleukin and conventional IL-2-based immunocytokines. Oncoimmunology (2017)

Release Date

2017-05-03

Peptides

Interleukin-2 receptor subunit beta: A
Cytokine receptor common subunit gamma: B
Interleukin-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

Interleukin-2 receptor subunit beta

Cytokine receptor common subunit gamma

Interleukin-2