SMTL ID : 6mkb.1 (1 other biounit)

Crystal structure of murine 4-1BB ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.1: 5 residues within 4Å: Chain A: N.23, W.82, A.137, Y.138, Y.146 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.82

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 5 residues within 4Å: Chain B: N.23, W.82, A.137, Y.138, Y.146 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.82

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

NA.3: 6 residues within 4Å: Chain A: T.25, L.26, W.28, K.50, S.132, V.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.133, A:V.133 NA.4: 6 residues within 4Å: Chain A: K.67, S.69, E.150, L.151, S.152, N.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.69, A:E.150, A:S.152 Water bridges: A:T.157 NA.9: 6 residues within 4Å: Chain B: K.67, S.69, E.150, L.151, S.152, N.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.67, B:S.69, B:S.152

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

SO4.5: 3 residues within 4Å: Chain B: K.16, H.29, Q.31 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.31 Water bridges: B:K.16, B:K.16, B:S.30, B:S.30 Salt bridges: B:K.16, B:H.29 SO4.6: 3 residues within 4Å: Chain B: F.106, P.107, C.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.108 SO4.7: 3 residues within 4Å: Chain B: K.16, N.17, H.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.17 Salt bridges: B:H.29 SO4.8: 4 residues within 4Å: Chain B: T.75, H.77, E.111, N.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.112 Salt bridges: B:H.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bitra, A. et al., Crystal structure of the m4-1BB/4-1BBL complex reveals an unusual dimeric ligand that undergoes structural changes upon 4-1BB receptor binding. J. Biol. Chem. (2019)

Release Date

2018-12-19

Peptides

Tumor necrosis factor ligand superfamily member 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tumor necrosis factor ligand superfamily member 9

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