SMTL ID : 3vsn.1

The crystal structure of novel chondroition lyase ODV-E66, baculovirus envelope protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

75 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 2 residues within 4Å: Chain A: I.539 Ligands: GOL.29 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: P.316, L.317 Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: E.626, P.627, A.628, L.629 Ligand excluded by PLIP IOD.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: S.166 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: N.619 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: N.607 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: E.574 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: K.433, N.439, E.463 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: N.301, N.355 Ligand excluded by PLIP IOD.11: 6 residues within 4Å: Chain A: A.251, Y.252, G.253, M.298, S.299 Ligands: GOL.28 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: S.47 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain A: P.289, T.314, Y.315 Ligands: IOD.54 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: W.60, N.108 Ligand excluded by PLIP IOD.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: R.36, K.39, N.156 Ligand excluded by PLIP IOD.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain A: N.486 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: E.51, H.83, H.139 Ligand excluded by PLIP IOD.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain A: N.235, H.246 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain A: K.333, H.451 Ligand excluded by PLIP IOD.31: 1 residues within 4Å: Chain A: T.280 Ligand excluded by PLIP IOD.32: 1 residues within 4Å: Chain A: T.276 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain A: G.253, Y.254, N.257 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Chain A: R.214 Ligand excluded by PLIP IOD.35: 2 residues within 4Å: Chain A: L.167, W.171 Ligand excluded by PLIP IOD.36: 3 residues within 4Å: Chain A: S.70, W.72, T.73 Ligand excluded by PLIP IOD.37: 3 residues within 4Å: Chain A: P.56, N.57, R.58 Ligand excluded by PLIP IOD.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain A: F.637, V.638 Ligand excluded by PLIP IOD.40: 1 residues within 4Å: Chain A: H.451 Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Chain A: L.488, N.496 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain A: L.488, S.489, A.492 Ligand excluded by PLIP IOD.43: 1 residues within 4Å: Chain A: G.560 Ligand excluded by PLIP IOD.44: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.45: 4 residues within 4Å: Chain A: R.58, N.59, D.67 Ligands: IOD.46 Ligand excluded by PLIP IOD.46: 3 residues within 4Å: Chain A: R.58, N.68 Ligands: IOD.45 Ligand excluded by PLIP IOD.47: 2 residues within 4Å: Chain A: N.59, W.60 Ligand excluded by PLIP IOD.48: 2 residues within 4Å: Chain A: N.63, W.72 Ligand excluded by PLIP IOD.49: 1 residues within 4Å: Chain A: H.186 Ligand excluded by PLIP IOD.50: 3 residues within 4Å: Chain A: P.177, N.181, G.184 Ligand excluded by PLIP IOD.51: 3 residues within 4Å: Chain A: R.169, R.206 Ligands: IOD.52 Ligand excluded by PLIP IOD.52: 2 residues within 4Å: Chain A: R.206 Ligands: IOD.51 Ligand excluded by PLIP IOD.53: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.54: 4 residues within 4Å: Chain A: G.310, I.313 Ligands: IOD.13, GOL.23 Ligand excluded by PLIP IOD.55: 2 residues within 4Å: Chain A: N.301, T.303 Ligand excluded by PLIP IOD.56: 1 residues within 4Å: Chain A: N.377 Ligand excluded by PLIP IOD.57: 1 residues within 4Å: Chain A: N.307 Ligand excluded by PLIP IOD.58: 2 residues within 4Å: Chain A: V.54, N.307 Ligand excluded by PLIP IOD.59: 2 residues within 4Å: Chain A: R.374, I.375 Ligand excluded by PLIP IOD.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.61: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.62: 2 residues within 4Å: Chain A: P.633, V.638 Ligand excluded by PLIP IOD.63: 2 residues within 4Å: Chain A: N.635, N.646 Ligand excluded by PLIP IOD.64: 2 residues within 4Å: Chain A: R.114, S.118 Ligand excluded by PLIP IOD.65: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.66: 7 residues within 4Å: Chain A: V.249, R.250, G.296, V.297, M.298, W.362 Ligands: GOL.28 Ligand excluded by PLIP IOD.67: 1 residues within 4Å: Chain A: A.435 Ligand excluded by PLIP IOD.68: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.69: 2 residues within 4Å: Chain A: M.398, N.438 Ligand excluded by PLIP IOD.70: 3 residues within 4Å: Chain A: N.468, N.469, Y.546 Ligand excluded by PLIP IOD.71: 2 residues within 4Å: Chain A: Q.543, Y.546 Ligand excluded by PLIP IOD.72: 2 residues within 4Å: Chain A: I.256, N.257 Ligand excluded by PLIP IOD.73: 2 residues within 4Å: Chain A: N.520, P.522 Ligand excluded by PLIP IOD.74: 3 residues within 4Å: Chain A: D.609, T.610, T.611 Ligand excluded by PLIP IOD.75: 2 residues within 4Å: Chain A: R.527, S.528 Ligand excluded by PLIP IOD.76: 4 residues within 4Å: Chain A: N.381, N.530, S.531, S.532 Ligand excluded by PLIP IOD.77: 1 residues within 4Å: Chain A: N.571 Ligand excluded by PLIP IOD.78: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.79: 3 residues within 4Å: Chain A: Q.416, N.607, E.608 Ligand excluded by PLIP IOD.80: 2 residues within 4Å: Chain A: G.583, K.585 Ligand excluded by PLIP IOD.81: 3 residues within 4Å: Chain A: R.513, S.523 Ligands: IOD.82 Ligand excluded by PLIP IOD.82: 5 residues within 4Å: Chain A: E.502, R.513, S.523, L.524 Ligands: IOD.81 Ligand excluded by PLIP IOD.83: 1 residues within 4Å: Chain A: P.627 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 6 residues within 4Å: Chain A: Y.44, N.311, F.312, I.313, T.314 Ligands: IOD.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.311, A:T.314 GOL.24: 4 residues within 4Å: Chain A: L.629, Q.630, I.658, V.659 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.630, A:V.659 GOL.25: 3 residues within 4Å: Chain A: N.518, I.519, N.520 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.518, A:N.520 Water bridges: A:N.518, A:I.519, A:V.521, A:V.521 GOL.26: 5 residues within 4Å: Chain A: T.610, K.644, L.645, N.647, S.648 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.644, A:S.648, A:S.648 Water bridges: A:N.647, A:T.649 GOL.27: 5 residues within 4Å: Chain A: V.319, K.421, T.422, D.423, K.600 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.319, A:D.423 Water bridges: A:V.319, A:K.421, A:K.421 GOL.28: 11 residues within 4Å: Chain A: D.245, H.246, V.249, R.250, A.251, M.298, R.300, E.350, W.362 Ligands: IOD.11, IOD.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.246, A:M.298, A:R.300 GOL.29: 3 residues within 4Å: Chain A: P.522, I.539 Ligands: IOD.1 No protein-ligand interaction detected (PLIP) GOL.30: 2 residues within 4Å: Chain A: N.57, N.59 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawaguchi, Y. et al., The crystal structure of novel chondroition lyase ODV-E66, baculovirus envelope protein. To be Published

Release Date

2013-05-22

Peptides

Occlusion-derived virus envelope protein E66: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Occlusion-derived virus envelope protein E66

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