SMTL ID : 5ogi.1

Complex of a binding protein and human adenovirus C 5 hexon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: T.58, D.59, R.60, A.623, H.624, N.625 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.58, A:D.59, A:H.624 Salt bridges: A:H.624 SO4.2: 3 residues within 4Å: Chain A: N.422, R.453, F.458 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.422, A:N.422 Salt bridges: A:R.453 SO4.3: 3 residues within 4Å: Chain A: A.139, K.165, H.167 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.167 Salt bridges: A:K.165, A:H.167 SO4.4: 2 residues within 4Å: Chain A: F.795, R.796 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.796 SO4.5: 4 residues within 4Å: Chain A: Q.62, R.63, L.66, R.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.63 Salt bridges: A:R.63, A:R.92 SO4.6: 4 residues within 4Å: Chain A: S.25, P.26, G.27, L.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.25, A:S.25, A:G.27, A:L.28 SO4.7: 5 residues within 4Å: Chain A: T.381, V.391, S.393, M.791, R.868 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.393, A:S.393, A:Y.394 Salt bridges: A:R.868

10 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.8: 8 residues within 4Å: Chain A: P.111, T.112, F.113, K.114, P.296, D.297, N.322, Y.501 No protein-ligand interaction detected (PLIP) DIO.9: 5 residues within 4Å: Chain A: K.486, Y.487, S.488, R.507 Ligands: DIO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.488, A:R.507 DIO.10: 6 residues within 4Å: Chain A: Y.174, I.186, Q.201, P.202, E.203, I.206 No protein-ligand interaction detected (PLIP) DIO.11: 2 residues within 4Å: Chain A: H.932, R.933 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.933 DIO.12: 5 residues within 4Å: Chain A: Y.487, L.820, L.832 Ligands: DIO.9, DIO.15 No protein-ligand interaction detected (PLIP) DIO.13: 5 residues within 4Å: Chain A: P.70, R.73, D.611, S.612, I.613 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.613 DIO.14: 5 residues within 4Å: Chain A: R.670, N.671, P.944, F.945, S.946 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.670, A:S.946 DIO.15: 9 residues within 4Å: Chain A: L.485, K.486, Y.487, A.510, L.513, I.819, L.820, L.832 Ligands: DIO.12 No protein-ligand interaction detected (PLIP) DIO.16: 5 residues within 4Å: Chain A: I.177, N.178, E.215, N.217, H.218 No protein-ligand interaction detected (PLIP) DIO.22: 4 residues within 4Å: Chain B: V.11, T.13, K.32, S.34 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.13

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.17: 4 residues within 4Å: Chain A: Y.174, S.175, G.176, I.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.175

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.18: 7 residues within 4Å: Chain A: N.519, W.524, L.526, D.527, Y.528, R.803, V.805 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.527 Water bridges: A:Q.861 Salt bridges: A:R.803 MES.19: 8 residues within 4Å: Chain A: G.378, D.379, R.380, S.786, Y.787, D.789, R.790, R.796 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.379, A:R.790 MES.20: 4 residues within 4Å: Chain A: D.395, F.472, R.539, R.544 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.539, A:R.539 Salt bridges: A:R.539 MES.21: 4 residues within 4Å: Chain A: Y.212, E.213, T.214, E.215 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmid, M. et al., Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control. Nat Commun (2018)

Release Date

2018-02-07

Peptides

Hexon protein: A
scFv of 9C12 antibody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hexon protein

scFv of 9C12 antibody

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