SMTL ID : 2xe4.1

Structure of Oligopeptidase B from Leishmania major

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x FC0- ARG- VAL- RGL: ANTIPAIN(Non-covalent)

FC0-ARG-VAL-RGL.1: 16 residues within 4Å: Chain A: R.245, E.246, S.273, Y.516, Y.519, S.597, A.598, F.623, T.629, M.630, L.637, E.641, R.684, V.685, H.717 Ligands: PO4.61 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.519, A:Y.519, A:L.637, A:V.685 Hydrogen bonds: A:S.273, A:Y.516, A:Y.519, A:Y.519, A:A.598, A:R.684, A:R.684, A:R.684 Water bridges: A:L.244, A:S.273, A:L.637, A:L.637, A:T.638, A:G.640, A:A.686, A:E.689 Salt bridges: A:E.641, A:E.689 pi-Cation interactions: A:F.623

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: P.611, D.612, F.614, E.670, Y.671, P.672, N.705 Ligands: PGR.36, PGR.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.612, A:N.705 GOL.3: 7 residues within 4Å: Chain A: H.360, V.361, V.404, F.405, K.406, A.407 Ligands: PGR.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.361, A:A.407 Water bridges: A:G.408 GOL.4: 7 residues within 4Å: Chain A: G.472, N.477, H.500, D.536, R.746, L.747, L.748 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.500, A:D.536, A:L.748 Water bridges: A:Y.478, A:Y.478, A:Y.478, A:Y.478 GOL.5: 6 residues within 4Å: Chain A: K.615, N.673, N.705, H.740, K.742 Ligands: PGR.37 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.615, A:N.673, A:N.705, A:H.740 Water bridges: A:N.705 GOL.6: 5 residues within 4Å: Chain A: R.596, F.718, F.726 Ligands: PGR.47, PGR.49 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.721 GOL.7: 4 residues within 4Å: Chain A: R.412, Q.457, D.458, H.459 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.457 Water bridges: A:T.395 GOL.8: 5 residues within 4Å: Chain A: P.448, V.466, R.467, E.468, V.469 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.467, A:V.469 Water bridges: A:V.469, A:G.470 GOL.9: 6 residues within 4Å: Chain A: A.485, T.486, A.575, E.578, F.579, N.582 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.486, A:N.582 GOL.10: 3 residues within 4Å: Chain A: L.564, D.655, Y.656 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.655 Water bridges: A:D.655 GOL.11: 7 residues within 4Å: Chain A: K.319, Y.563, W.642, E.643, N.647, E.650, Y.653 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.319, A:N.647 Water bridges: A:E.650, A:E.650

48 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.12: 7 residues within 4Å: Chain A: Y.514, E.594, G.595, L.618, G.620, Q.733 Ligands: PGO.13 Ligand excluded by PLIP PGR.14: 7 residues within 4Å: Chain A: H.328, G.329, S.331, H.332, G.403, V.404 Ligands: PGR.27 Ligand excluded by PLIP PGR.15: 5 residues within 4Å: Chain A: A.720, K.721, R.723, F.726, W.727 Ligand excluded by PLIP PGR.16: 7 residues within 4Å: Chain A: W.70, R.72, D.73, D.78, V.81 Ligands: PGR.45, PGR.50 Ligand excluded by PLIP PGR.17: 4 residues within 4Å: Chain A: R.547, A.555, W.556, G.560 Ligand excluded by PLIP PGR.18: 4 residues within 4Å: Chain A: D.175, Y.201, F.718, K.721 Ligand excluded by PLIP PGR.19: 8 residues within 4Å: Chain A: G.389, L.390, R.482, P.494, S.496, P.525, H.545, E.551 Ligand excluded by PLIP PGR.20: 5 residues within 4Å: Chain A: A.108, E.109, S.112, H.113, G.471 Ligand excluded by PLIP PGR.21: 7 residues within 4Å: Chain A: Y.123, Y.130, Y.143, I.161, V.179, P.181, L.431 Ligand excluded by PLIP PGR.22: 5 residues within 4Å: Chain A: I.162, D.163, Q.166, V.167, K.206 Ligand excluded by PLIP PGR.23: 5 residues within 4Å: Chain A: Y.125, K.278, A.279, T.282 Ligands: PGR.31 Ligand excluded by PLIP PGR.24: 4 residues within 4Å: Chain A: P.230, T.282, N.283, L.302 Ligand excluded by PLIP PGR.25: 6 residues within 4Å: Chain A: G.320, V.321, N.338, E.339, G.340, G.341 Ligand excluded by PLIP PGR.26: 6 residues within 4Å: Chain A: R.322, Y.323, D.324, L.336, T.337, H.345 Ligand excluded by PLIP PGR.27: 5 residues within 4Å: Chain A: D.281, N.283, G.329, Y.433 Ligands: PGR.14 Ligand excluded by PLIP PGR.28: 4 residues within 4Å: Chain A: D.301, R.303, T.330, R.352 Ligand excluded by PLIP PGR.29: 6 residues within 4Å: Chain A: H.332, I.349, A.350, P.351, H.360 Ligands: GOL.3 Ligand excluded by PLIP PGR.30: 5 residues within 4Å: Chain A: M.397, A.398, D.399, S.400, T.409 Ligand excluded by PLIP PGR.31: 8 residues within 4Å: Chain A: Y.125, A.280, D.281, T.282, L.431, E.432, Y.433 Ligands: PGR.23 Ligand excluded by PLIP PGR.32: 5 residues within 4Å: Chain A: T.437, D.453, S.460, R.461, T.462 Ligand excluded by PLIP PGR.33: 3 residues within 4Å: Chain A: H.459, S.460, R.461 Ligand excluded by PLIP PGR.34: 6 residues within 4Å: Chain A: Y.514, M.523, D.524, Q.526, I.543 Ligands: PGR.49 Ligand excluded by PLIP PGR.35: 6 residues within 4Å: Chain A: R.467, S.528, I.529, Q.530, W.727 Ligands: PGR.49 Ligand excluded by PLIP PGR.36: 6 residues within 4Å: Chain A: P.588, S.589, F.614, K.615 Ligands: GOL.2, PGR.52 Ligand excluded by PLIP PGR.37: 7 residues within 4Å: Chain A: R.95, N.673, N.704, N.705, E.706, H.740 Ligands: GOL.5 Ligand excluded by PLIP PGR.38: 4 residues within 4Å: Chain A: V.124, E.432, E.435, P.436 Ligand excluded by PLIP PGR.39: 3 residues within 4Å: Chain A: Y.277, D.324, Q.326 Ligand excluded by PLIP PGR.40: 3 residues within 4Å: Chain A: Y.123, S.428, Q.429 Ligand excluded by PLIP PGR.41: 4 residues within 4Å: Chain A: A.37, K.39, W.70, A.80 Ligand excluded by PLIP PGR.42: 3 residues within 4Å: Chain A: R.76, I.82, M.713 Ligand excluded by PLIP PGR.43: 3 residues within 4Å: Chain A: R.315, E.339, W.358 Ligand excluded by PLIP PGR.44: 3 residues within 4Å: Chain A: R.483, F.484, F.579 Ligand excluded by PLIP PGR.45: 6 residues within 4Å: Chain A: F.69, R.72, D.73, D.74 Ligands: PGR.16, PGR.50 Ligand excluded by PLIP PGR.46: 2 residues within 4Å: Chain A: K.465, V.466 Ligand excluded by PLIP PGR.47: 9 residues within 4Å: Chain A: Q.530, Q.677, S.719, F.726, E.729, S.730, Q.733 Ligands: GOL.6, PGO.13 Ligand excluded by PLIP PGR.48: 7 residues within 4Å: Chain A: D.52, G.54, P.55, N.269, P.270, L.271, W.642 Ligand excluded by PLIP PGR.49: 7 residues within 4Å: Chain A: Q.526, F.527, S.528 Ligands: GOL.6, PGR.34, PGR.35, PO4.63 Ligand excluded by PLIP PGR.50: 5 residues within 4Å: Chain A: D.73, D.74, D.75 Ligands: PGR.16, PGR.45 Ligand excluded by PLIP PGR.51: 2 residues within 4Å: Chain A: K.304 Ligands: PGR.57 Ligand excluded by PLIP PGR.52: 6 residues within 4Å: Chain A: E.670, D.703, N.704, N.705 Ligands: GOL.2, PGR.36 Ligand excluded by PLIP PGR.53: 6 residues within 4Å: Chain A: D.74, R.76, E.242, L.244, P.636, W.688 Ligand excluded by PLIP PGR.54: 4 residues within 4Å: Chain A: D.664, N.665, V.666, R.667 Ligand excluded by PLIP PGR.55: 4 residues within 4Å: Chain A: N.86, K.89, V.90, Q.93 Ligand excluded by PLIP PGR.56: 2 residues within 4Å: Chain A: L.362, A.407 Ligand excluded by PLIP PGR.57: 5 residues within 4Å: Chain A: D.301, K.304, H.308, E.312 Ligands: PGR.51 Ligand excluded by PLIP PGR.58: 3 residues within 4Å: Chain A: Y.478, K.479, V.480 Ligand excluded by PLIP PGR.59: 2 residues within 4Å: Chain A: C.263, E.266 Ligand excluded by PLIP PGR.60: 4 residues within 4Å: Chain A: A.388, G.389, F.484, L.552 Ligand excluded by PLIP

1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.13: 9 residues within 4Å: Chain A: Q.530, Y.534, E.594, L.618, S.730, Q.733, Q.734 Ligands: PGR.12, PGR.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.534, A:Y.534, A:E.594

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.61: 9 residues within 4Å: Chain A: Y.516, R.596, S.597, R.684, H.717, F.718 Ligands: FC0-ARG-VAL-RGL.1, FC0-ARG-VAL-RGL.1, PO4.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.597 Salt bridges: A:R.596, A:H.717 PO4.62: 5 residues within 4Å: Chain A: V.200, G.221, K.240, D.241, L.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.240, A:K.240 Water bridges: A:K.240 PO4.63: 7 residues within 4Å: Chain A: Y.514, Y.516, L.521, M.523, R.596 Ligands: PGR.49, PO4.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.514, A:R.596

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.64: 2 residues within 4Å: Chain A: V.227, W.228 Ligand excluded by PLIP CL.66: 3 residues within 4Å: Chain A: Y.140, K.141, V.164 Ligand excluded by PLIP CL.68: 5 residues within 4Å: Chain A: H.328, H.332, I.349, V.404, F.405 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain A: E.83, N.86 Ligand excluded by PLIP

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

NA.65: 3 residues within 4Å: Chain A: I.111, S.112, I.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.111 Water bridges: A:E.116 NA.67: 4 residues within 4Å: Chain A: D.194, S.196, N.198, V.200 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.194, A:S.196, A:N.198, A:V.200 Water bridges: A:M.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mcluskey, K. et al., Crystal Structure of Leishmania Major Oligopeptidase B Gives Insight Into the Enzymatic Properties of a Trypanosomatid Virulence Factor. J.Biol.Chem. (2010)

Release Date

2010-10-06

Peptides

OLIGOPEPTIDASE B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

OLIGOPEPTIDASE B