SMTL ID : 6cfq.1

Crystal structure of the D141N variant of catalase-peroxidase from B. pseudomallei with INH bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: G.84, L.85, I.87, R.88, W.91, V.219, P.221, F.241, L.254, I.255, G.258, H.259, F.261, G.262, K.263, T.264, H.265, T.303, S.304, L.306, W.310, L.366, T.368, F.396, W.400 Ligands: OXY.4, OXY.8 28 PLIP interactions: 27 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:I.87, A:W.91, A:W.91, A:W.91, A:F.241, A:L.254, A:I.255, A:I.255, A:T.264, A:L.306, A:W.310, A:L.366, A:F.396, A:W.400 Hydrogen bonds: A:K.263, A:H.265, A:S.304 Water bridges: A:D.78, A:D.78, A:G.84, A:R.88, A:H.265 Salt bridges: A:R.88, A:H.265, A:H.265 pi-Stacking: A:W.91 Metal complexes: A:H.259, H2O.1 HEM.9: 27 residues within 4Å: Chain B: G.84, L.85, I.87, R.88, W.91, V.219, P.221, F.241, L.254, I.255, G.258, H.259, F.261, G.262, K.263, T.264, H.265, T.303, S.304, L.306, W.310, L.366, T.368, F.396, W.400 Ligands: OXY.12, OXY.15 30 PLIP interactions: 29 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.87, B:R.88, B:W.91, B:W.91, B:W.91, B:P.221, B:F.241, B:L.254, B:I.255, B:I.255, B:T.264, B:L.306, B:W.310, B:W.310, B:L.366, B:F.396, B:W.400 Hydrogen bonds: B:K.263, B:H.265, B:T.303, B:S.304 Water bridges: B:G.84, B:R.88, B:H.265 Salt bridges: B:R.88, B:H.265, B:H.265 pi-Stacking: B:W.91 Metal complexes: B:H.259, H2O.32

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

NA.2: 5 residues within 4Å: Chain A: G.102, R.103, G.104, D.407, S.474 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.407, A:D.407 Water bridges: A:E.108 NA.10: 4 residues within 4Å: Chain B: G.102, R.103, G.104, S.474 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.102

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

CL.3: 3 residues within 4Å: Chain A: G.104, E.178, V.180 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: G.104, E.178, V.180 Ligands: NIZ.17 Ligand excluded by PLIP

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 5 residues within 4Å: Chain A: R.88, H.92, N.121 Ligands: HEM.1, OXY.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.88, A:R.88, A:N.121 Water bridges: A:H.92 OXY.8: 6 residues within 4Å: Chain A: W.91, H.92, N.121, I.217 Ligands: HEM.1, OXY.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.92 Water bridges: A:N.121, A:N.121, A:I.217, A:Y.218, A:Y.218, A:Y.218 OXY.12: 5 residues within 4Å: Chain B: R.88, H.92, N.121 Ligands: HEM.9, OXY.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.88, B:H.92, B:N.121 OXY.15: 4 residues within 4Å: Chain B: W.91, H.92 Ligands: HEM.9, OXY.12 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.91, B:N.121 Water bridges: B:N.121, B:N.121, B:I.217, B:Y.218, B:Y.218

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

PO4.5: 3 residues within 4Å: Chain A: K.360, H.361, R.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.362 Salt bridges: A:H.361, A:R.362 PO4.13: 3 residues within 4Å: Chain B: K.360, H.361, R.362 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.360, B:R.362 Salt bridges: B:H.361, B:R.362

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

MPD.6: 6 residues within 4Å: Chain A: P.120, A.123, L.189, W.289, T.303, S.304 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.189 Hydrogen bonds: A:W.289, A:T.303 MPD.7: 3 residues within 4Å: Chain A: D.63, P.134, K.138 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.63, A:K.138 Hydrogen bonds: A:P.134 MPD.14: 6 residues within 4Å: Chain B: P.120, A.123, A.270, W.289, T.303, S.304 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.270 Hydrogen bonds: B:W.289 MPD.16: 4 residues within 4Å: Chain B: W.330, W.342, L.370, F.374 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.342, B:L.370, B:F.374 Water bridges: B:W.330

1 x NIZ: pyridine-4-carbohydrazide(Non-covalent)

NIZ.17: 11 residues within 4Å: Chain B: R.103, E.108, E.178, D.179, V.180, G.473, S.474, Q.602, L.603, T.605 Ligands: CL.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.103, B:R.103, B:E.178, B:Q.602 Water bridges: B:G.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loewen, P.C., Crystal structure of the D141N variant of catalase-peroxidase from B. pseudomallei with INH bound. To be published

Release Date

2018-02-28

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase