SMTL ID : 2obe.1

Crystal Structure of Chimpanzee Adenovirus (Type 68/Simian 25) Major Coat Protein Hexon

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

22 x 2HP: DIHYDROGENPHOSPHATE ION(Non-covalent)

2HP.1: 6 residues within 4Å: Chain A: T.57, D.58, R.59, A.603, H.604, N.605 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.57, A:D.58, A:D.58, A:H.604, A:N.605, A:N.605 Water bridges: A:R.59 Salt bridges: A:R.59, A:H.604 2HP.2: 4 residues within 4Å: Chain A: P.110, S.111, Y.481, D.482 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.833, A:P.110 2HP.3: 4 residues within 4Å: Chain A: D.730, N.735, K.842 Chain C: H.539 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.730, A:N.735 Water bridges: A:K.842, C:H.539 Salt bridges: A:K.842, C:H.539 2HP.4: 4 residues within 4Å: Chain A: E.611, R.615, H.912, R.913 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.913 Salt bridges: A:R.615, A:H.912 2HP.5: 5 residues within 4Å: Chain A: T.362, V.372, S.374, M.771, R.848 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.374, A:R.848 Salt bridges: A:R.848 2HP.13: 4 residues within 4Å: Chain A: H.539 Chain B: D.730, N.735, K.842 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.730, B:D.730, B:N.735 Water bridges: B:R.727, B:T.728 Salt bridges: B:K.842, A:H.539 2HP.14: 5 residues within 4Å: Chain B: R.650, N.651, P.924, F.925, S.926 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.651, B:N.651, B:F.925, B:S.926 Water bridges: B:R.650 2HP.15: 6 residues within 4Å: Chain B: T.57, D.58, R.59, A.603, H.604, N.605 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.58, B:H.604, B:N.605 Salt bridges: B:R.59, B:H.604 2HP.16: 4 residues within 4Å: Chain B: D.360, R.363 Chain C: E.765, G.766 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:D.360, C:G.766 Water bridges: B:R.363, C:P.764, C:Y.767, C:Y.767 2HP.17: 7 residues within 4Å: Chain B: N.755, Q.759, Y.762, M.860 Chain C: T.36, Y.37, S.39 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.36, B:Y.762 2HP.18: 6 residues within 4Å: Chain B: E.611, R.615, P.911, H.912, R.913 Ligands: 2HP.21 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.913 Water bridges: B:R.913 Salt bridges: B:R.615, B:H.912, B:R.913 2HP.19: 2 residues within 4Å: Chain B: R.519 Chain C: H.385 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.519, C:H.385 2HP.20: 2 residues within 4Å: Chain B: P.911, H.912 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.909, B:E.917 Salt bridges: B:H.912 2HP.21: 4 residues within 4Å: Chain B: S.608, E.611, A.612 Ligands: 2HP.18 No protein-ligand interaction detected (PLIP) 2HP.22: 6 residues within 4Å: Chain B: T.665, K.666, T.668, D.676, Y.678, F.679 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.668, B:T.668 2HP.23: 5 residues within 4Å: Chain B: A.875, N.876, S.877, H.879 Ligands: MPD.36 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.876, B:S.877, B:S.877 Salt bridges: B:H.879 2HP.24: 8 residues within 4Å: Chain B: I.498, N.499, W.504, L.506, D.507, P.508, R.783 Ligands: MPD.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.499, B:D.507, B:D.507 Salt bridges: B:R.783 2HP.37: 4 residues within 4Å: Chain B: H.539 Chain C: D.730, N.735, K.842 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Salt bridges: B:H.539, C:K.842 Hydrogen bonds: C:D.730, C:N.735 2HP.38: 4 residues within 4Å: Chain A: K.833 Chain C: P.110, Y.481, D.482 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.482, A:K.833 Water bridges: C:N.485 2HP.39: 4 residues within 4Å: Chain A: E.765, G.766 Chain C: D.360, R.363 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.360, C:D.360, A:G.766 Water bridges: C:D.360, C:R.363, A:Y.767 2HP.40: 6 residues within 4Å: Chain C: N.499, W.504, L.506, D.507, P.508, R.783 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.499, C:W.504, C:D.507 Salt bridges: C:R.783 2HP.41: 6 residues within 4Å: Chain C: T.57, D.58, R.59, A.603, H.604, N.605 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.57, C:T.57, C:T.57, C:D.58, C:H.604, C:N.605 Salt bridges: C:R.59, C:H.604

24 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 4 residues within 4Å: Chain A: L.23, A.31, D.35, G.41 Ligand excluded by PLIP MPD.7: 8 residues within 4Å: Chain A: V.512, N.513, N.516, K.664, K.666, E.667, Y.681, Y.693 Ligand excluded by PLIP MPD.8: 4 residues within 4Å: Chain A: Y.465, K.466, Y.467, L.799 Ligand excluded by PLIP MPD.9: 8 residues within 4Å: Chain A: N.624, D.625, Y.626, S.628, R.656, A.864, V.902, F.903 Ligand excluded by PLIP MPD.10: 5 residues within 4Å: Chain A: G.359, D.360, R.363 Chain B: E.765, G.766 Ligand excluded by PLIP MPD.11: 4 residues within 4Å: Chain A: Q.795 Chain C: N.226, K.227, E.228 Ligand excluded by PLIP MPD.12: 5 residues within 4Å: Chain A: N.253, R.254, S.255 Chain C: D.405, T.406 Ligand excluded by PLIP MPD.25: 5 residues within 4Å: Chain B: N.226, K.227, E.228, K.242 Chain C: Q.795 Ligand excluded by PLIP MPD.26: 4 residues within 4Å: Chain B: S.20, A.31, D.35, G.41 Ligand excluded by PLIP MPD.27: 2 residues within 4Å: Chain B: P.69, R.72 Ligand excluded by PLIP MPD.28: 8 residues within 4Å: Chain B: V.512, N.513, N.516, K.664, K.666, E.667, Y.681, Y.693 Ligand excluded by PLIP MPD.29: 5 residues within 4Å: Chain B: S.464, Y.465, K.466, Y.467, L.799 Ligand excluded by PLIP MPD.30: 8 residues within 4Å: Chain A: R.45 Chain B: N.624, D.625, Y.626, S.628, R.656, A.864, F.903 Ligand excluded by PLIP MPD.31: 4 residues within 4Å: Chain B: P.110, Y.481, D.482 Chain C: K.833 Ligand excluded by PLIP MPD.32: 5 residues within 4Å: Chain B: L.493, I.498, L.506, Y.826 Ligands: 2HP.24 Ligand excluded by PLIP MPD.33: 3 residues within 4Å: Chain B: L.448, W.449, F.452 Ligand excluded by PLIP MPD.34: 2 residues within 4Å: Chain B: N.413, T.418 Ligand excluded by PLIP MPD.35: 5 residues within 4Å: Chain B: D.71, E.73, K.80, R.82, E.562 Ligand excluded by PLIP MPD.36: 6 residues within 4Å: Chain B: F.705, V.709, F.855, M.872, H.879 Ligands: 2HP.23 Ligand excluded by PLIP MPD.42: 7 residues within 4Å: Chain A: T.36, Y.37, S.39 Chain C: N.755, Q.759, Y.762, M.860 Ligand excluded by PLIP MPD.43: 6 residues within 4Å: Chain C: L.23, A.31, R.32, D.35, G.41, F.44 Ligand excluded by PLIP MPD.44: 7 residues within 4Å: Chain C: V.512, N.513, N.516, K.664, K.666, E.667, Y.693 Ligand excluded by PLIP MPD.45: 4 residues within 4Å: Chain C: Y.465, Y.467, L.799, L.812 Ligand excluded by PLIP MPD.46: 7 residues within 4Å: Chain C: N.624, D.625, Y.626, S.628, R.656, A.864, F.903 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pichla-Gollon, S.L. et al., Structure-based identification of a major neutralizing site in an adenovirus hexon. J.Virol. (2007)

Release Date

2007-07-24

Peptides

Hexon protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hexon protein