SMTL ID : 4nvm.1

Predicting protein conformational response in prospective ligand discovery

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

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

HEM.1: 23 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: 2O0.3, MES.4 27 PLIP interactions: 26 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:P.142, A:A.144, A:F.155, A:L.168, A:A.171, A:T.177, A:L.227 Hydrogen bonds: A:K.176, A:H.178, A:N.181 Water bridges: A:Y.33, A:R.45, 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 pi-Cation interactions: A:R.45 Metal complexes: A:H.172, H2O.7

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

PO4.2: 3 residues within 4Å: Chain A: L.27, M.116, N.191 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.27, A:N.191 Water bridges: A:Y.39, A:G.40, A:G.40, A:E.115

1 x 2O0: 3-(1H-benzimidazol-1-yl)propanamide(Non-covalent)

2O0.3: 14 residues within 4Å: Chain A: H.172, L.174, G.175, K.176, T.177, G.188, N.200, Y.224, M.225, M.226, L.227, D.230 Ligands: HEM.1, MES.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.172, A:T.177, A:L.227 Hydrogen bonds: A:N.200, A:M.225 pi-Stacking: A:H.172

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

MES.4: 11 residues within 4Å: Chain A: H.172, L.174, G.175, T.177, G.188, N.200, Y.224, M.225, M.226 Ligands: HEM.1, 2O0.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.200, A:M.225, A:M.225 Water bridges: A:T.177

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
B

Cytochrome c peroxidase

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