SMTL ID : 4e37.1

Crystal Structure of P. aeruginosa catalase, KatA tetramer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: R.50, M.52, H.53, R.90, G.109, F.110, S.111, V.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, S.335, Y.336, A.339, H.340, R.343 Chain B: L.39, D.43 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:H.53, A:V.124, A:N.126, A:P.136, A:F.139, A:F.139, A:F.139, A:F.139, A:F.139, A:L.277, A:R.332, A:Y.336, A:Y.336, A:A.339, B:L.39 Water bridges: A:R.50, A:S.111, A:F.312 Salt bridges: A:R.50, A:R.50, A:R.90, A:H.340, A:R.343 pi-Stacking: A:H.53, A:F.131, A:F.139 pi-Cation interactions: A:R.332 Metal complexes: A:Y.336 HEM.3: 26 residues within 4Å: Chain A: L.39, D.43 Chain B: R.50, M.52, H.53, R.90, G.109, F.110, S.111, V.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, S.335, Y.336, A.339, H.340, R.343 30 PLIP interactions: 29 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:H.53, B:V.124, B:N.126, B:P.136, B:F.139, B:F.139, B:F.139, B:F.139, B:F.139, B:L.277, B:R.332, B:Y.336, B:Y.336, B:A.339, A:L.39 Water bridges: B:S.111, B:A.310, B:F.312, B:A.339, B:R.343 Salt bridges: B:R.50, B:R.50, B:R.90, B:H.340, B:R.343 pi-Stacking: B:H.53, B:F.131, B:F.139 pi-Cation interactions: B:R.332 Metal complexes: B:Y.336 HEM.5: 26 residues within 4Å: Chain C: R.50, M.52, H.53, R.90, G.109, F.110, S.111, V.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, S.335, Y.336, A.339, H.340, R.343 Chain D: L.39, D.43 27 PLIP interactions: 26 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:H.53, C:V.124, C:N.126, C:P.136, C:F.139, C:F.139, C:F.139, C:F.139, C:L.277, C:R.332, C:Y.336, C:Y.336, C:A.339, D:L.39 Hydrogen bonds: C:S.111 Water bridges: C:S.111, C:A.310 Salt bridges: C:R.50, C:R.50, C:R.90, C:H.340, C:R.343 pi-Stacking: C:H.53, C:F.131, C:F.139 pi-Cation interactions: C:R.332 Metal complexes: C:Y.336 HEM.7: 26 residues within 4Å: Chain C: L.39, D.43 Chain D: R.50, M.52, H.53, R.90, G.109, F.110, S.111, V.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, S.335, Y.336, A.339, H.340, R.343 28 PLIP interactions: 27 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:H.53, D:V.124, D:N.126, D:P.136, D:F.139, D:F.139, D:F.139, D:F.139, D:L.277, D:R.332, D:Y.336, D:Y.336, D:A.339, C:L.39 Water bridges: D:R.51, D:S.111, D:A.310, D:R.343 Salt bridges: D:R.50, D:R.50, D:R.90, D:H.340, D:R.343 pi-Stacking: D:H.53, D:F.131, D:F.139 pi-Cation interactions: D:R.332 Metal complexes: D:Y.336

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 16 residues within 4Å: Chain A: P.129, H.172, I.176, S.179, R.181, H.191, H.213, V.280, W.281, P.282, H.283, Q.421, A.424, L.425, L.428, F.429 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.129 Hydrogen bonds: A:H.172, A:S.179, A:S.179, A:W.281, A:H.283 Water bridges: A:Q.260 Salt bridges: A:R.181, A:H.191, A:H.283, A:H.283 pi-Cation interactions: A:R.181, A:R.181 NDP.4: 16 residues within 4Å: Chain B: P.129, H.172, I.176, S.179, R.181, H.191, H.213, V.280, W.281, P.282, H.283, Q.421, A.424, L.425, L.428, F.429 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.129 Hydrogen bonds: B:S.179, B:S.179, B:W.281, B:H.283, B:Q.421 Water bridges: B:R.181, B:Q.260 Salt bridges: B:R.181, B:H.191, B:H.283, B:H.283 pi-Cation interactions: B:R.181 NDP.6: 16 residues within 4Å: Chain C: P.129, H.172, I.176, S.179, R.181, H.191, H.213, V.280, W.281, P.282, H.283, Q.421, A.424, L.425, L.428, F.429 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:P.129 Hydrogen bonds: C:H.172, C:S.179, C:S.179, C:W.281, C:H.283, C:L.425 Water bridges: C:Q.260, C:W.281 Salt bridges: C:R.181, C:H.191, C:H.283, C:H.283 pi-Cation interactions: C:R.181 NDP.8: 17 residues within 4Å: Chain D: P.129, H.172, I.176, S.179, R.181, H.191, H.213, Q.260, V.280, W.281, P.282, H.283, Q.421, A.424, L.425, L.428, F.429 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:P.129, D:V.280 Hydrogen bonds: D:S.179, D:S.179, D:W.281, D:H.283, D:Q.421 Water bridges: D:Q.260, D:W.281 Salt bridges: D:R.181, D:H.191, D:H.283, D:H.283 pi-Cation interactions: D:R.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, S. et al., KatA, the Major Catalase in Pseudomonas aeruginosa, Assists in Protecting Anaerobic Bacteria From Metabolic and Exogenous Nitric Oxide. To be Published

Release Date

2013-03-20

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase