SMTL ID : 4nvl.1

Predicting protein conformational response in prospective ligand discovery.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 22 residues within 4Å: Chain A: P.41, V.42, R.45, W.48, P.142, D.143, A.144, F.155, L.168, M.169, A.171, H.172, L.174, G.175, K.176, T.177, H.178, N.181, S.182, L.227, T.229 Ligands: 2NZ.2 28 PLIP interactions: 27 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:R.45, A:W.48, A:W.48, A:W.48, A:P.142, A:A.144, A:F.155, A:L.168, A:A.171, A:L.174, A:T.177 Hydrogen bonds: A:K.176, A:H.178, A:N.181, A:S.182 Water bridges: A:Y.33, A:D.34, A:D.34, A:D.34, A:R.45, A:G.81, A:H.178 Salt bridges: A:R.45, A:H.178, A:H.178 pi-Stacking: A:W.48 Metal complexes: A:H.172, H2O.2

2 x 2NZ: 1-(1H-benzimidazol-1-yl)propan-2-one(Non-covalent)

2NZ.2: 12 residues within 4Å: Chain A: H.172, A.173, L.174, G.175, K.176, T.177, F.197, M.225, M.226, L.227, D.230 Ligands: HEM.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.172, A:T.177, A:L.227 pi-Stacking: A:H.172 2NZ.6: 8 residues within 4Å: Chain A: F.86, L.89, E.90, H.93, K.94, S.101, L.104, F.105 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.86, A:F.86, A:L.89, A:E.90, A:K.94, A:L.104, A:F.105 Water bridges: A:K.94 pi-Stacking: A:H.93

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

PO4.3: 3 residues within 4Å: Chain A: Y.33, D.34, H.178 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.84 Water bridges: A:Y.33, A:D.34, A:D.34, A:N.181 Salt bridges: A:H.178 PO4.4: 5 residues within 4Å: Chain A: E.185, Q.217, D.219, G.223, Y.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.185, A:Q.217, A:D.219 Water bridges: A:G.188 PO4.5: 4 residues within 4Å: Chain A: L.27, E.115, M.116, N.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.115 Water bridges: A:Y.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fischer, M. et al., Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem (2014)

Release Date

2013-12-25

Peptides

Cytochrome c peroxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome c peroxidase

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