SMTL ID : 5syl.1

B. pseudomallei KatG with KCN bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: G.102, R.103, G.104, S.474 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.407, A:D.407 NA.8: 5 residues within 4Å: Chain B: G.102, R.103, G.104, D.407, S.474 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.102 Water bridges: B:G.104

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

CL.2: 3 residues within 4Å: Chain A: G.104, E.178, V.180 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: G.104, E.178, V.180 Ligand excluded by PLIP

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

HEM.3: 25 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, W.310, L.366, T.368, F.396, W.400 Ligands: CYN.4 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:I.87, A:W.91, A:W.91, A:P.221, A:F.241, A:L.254, A:I.255, A:I.255, A:T.264, 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:N.124, A:H.265 Salt bridges: A:R.88, A:H.265, A:H.265 pi-Stacking: A:W.91 Metal complexes: A:H.259 HEM.7: 25 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, W.310, L.366, T.368, F.396, W.400 Ligands: CYN.10 25 PLIP interactions: 25 interactions with chain B, Hydrophobic interactions: B:I.87, B:R.88, B:W.91, B:W.91, B:P.221, B:F.241, B:L.254, B:I.255, B:T.264, 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:R.88, B:N.124, B:H.265 Salt bridges: B:R.88, B:H.265, B:H.265 pi-Stacking: B:W.91 Metal complexes: B:H.259

2 x CYN: CYANIDE ION(Non-covalent)

CYN.4: 3 residues within 4Å: Chain A: W.91, H.92 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.92 CYN.10: 4 residues within 4Å: Chain B: R.88, W.91, H.92 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.92

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

MPD.5: 3 residues within 4Å: Chain A: D.63, P.134, I.135 No protein-ligand interaction detected (PLIP) MPD.6: 3 residues within 4Å: Chain A: P.120, W.289, T.303 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.120 Hydrogen bonds: A:T.303 MPD.11: 2 residues within 4Å: Chain B: R.486, E.509 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.509 Water bridges: B:Q.563 MPD.12: 1 residues within 4Å: Chain B: G.673 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.668 MPD.13: 5 residues within 4Å: Chain B: P.120, A.123, A.270, T.303, S.304 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.123, B:A.270 Hydrogen bonds: B:S.304

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

PO4.14: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loewen, P.C., Structure of B. pseudomallei KatG with cyanide bound. To be published

Release Date

2016-09-07

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

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