SMTL ID : 4blc.1

THE STRUCTURE OF ORTHORHOMBIC CRYSTALS OF BEEF LIVER CATALASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: R.71, V.72, V.73, H.74, R.111, G.130, F.131, V.145, G.146, N.147, F.160, G.215, S.216, H.217, L.298, F.333, M.349, R.353, A.356, Y.357, T.360, H.361, R.364 Chain D: M.60, D.64 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:V.72, A:V.73, A:H.74, A:V.145, A:N.147, A:F.160, A:F.160, A:F.160, A:F.160, A:L.298, A:R.353, A:A.356, A:Y.357, A:Y.357 Water bridges: A:V.72 Salt bridges: A:R.71, A:R.71, A:R.111, A:H.361, A:R.364 pi-Stacking: A:H.74, A:F.160 pi-Cation interactions: A:R.353 Metal complexes: A:Y.357 HEM.3: 26 residues within 4Å: Chain B: R.71, V.72, V.73, H.74, R.111, G.130, V.145, G.146, N.147, F.152, A.157, F.160, G.215, S.216, H.217, L.298, F.333, M.349, R.353, Y.357, T.360, H.361, R.364 Chain C: M.60, F.63, D.64 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:V.72, B:V.73, B:H.74, B:V.145, B:N.147, B:F.152, B:A.157, B:F.160, B:F.160, B:F.160, B:F.160, B:L.298, B:R.353, B:Y.357, B:Y.357, C:F.63 Salt bridges: B:R.71, B:R.71, B:R.111, B:H.361, B:R.364 pi-Stacking: B:H.74, B:F.160 pi-Cation interactions: B:R.353 Metal complexes: B:Y.357 HEM.5: 25 residues within 4Å: Chain B: M.60, D.64 Chain C: R.71, V.72, V.73, H.74, R.111, G.130, F.131, V.145, G.146, N.147, A.157, F.160, G.215, S.216, H.217, L.298, F.333, M.349, R.353, Y.357, T.360, H.361, R.364 25 PLIP interactions: 25 interactions with chain C, Hydrophobic interactions: C:V.72, C:V.73, C:H.74, C:N.147, C:A.157, C:F.160, C:F.160, C:F.160, C:L.298, C:R.353, C:Y.357, C:Y.357, C:T.360 Hydrogen bonds: C:V.72 Water bridges: C:A.132, C:T.360 Salt bridges: C:R.71, C:R.71, C:R.111, C:H.361, C:R.364 pi-Stacking: C:H.74, C:F.160 pi-Cation interactions: C:R.353 Metal complexes: C:Y.357 HEM.7: 25 residues within 4Å: Chain A: M.60, D.64 Chain D: R.71, V.72, V.73, H.74, R.111, G.130, A.132, V.145, G.146, N.147, F.152, A.157, F.160, S.216, L.298, F.333, M.349, R.353, A.356, Y.357, T.360, H.361, R.364 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:V.73, D:H.74, D:V.145, D:F.152, D:A.157, D:F.160, D:F.160, D:F.160, D:F.160, D:L.298, D:A.356, D:Y.357, D:Y.357 Water bridges: D:V.72 Salt bridges: D:R.71, D:R.71, D:R.111, D:H.361, D:R.364 pi-Stacking: D:H.74 pi-Cation interactions: D:R.353 Metal complexes: D:Y.357

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

NDP.2: 17 residues within 4Å: Chain A: P.150, H.193, F.197, R.202, D.212, Y.214, H.234, K.236, V.301, W.302, P.303, H.304, G.305, Q.441, T.444, F.445, V.449 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.150 Hydrogen bonds: A:H.193, A:S.200, A:Y.214, A:Y.214, A:K.236, A:W.302, A:H.304, A:H.304, A:G.305, A:F.445 Salt bridges: A:R.202, A:K.236, A:H.304 pi-Cation interactions: A:R.202, A:R.202 NDP.4: 20 residues within 4Å: Chain B: P.150, H.193, F.197, S.200, R.202, D.212, Y.214, H.234, K.236, I.241, V.301, W.302, P.303, H.304, G.305, Q.441, T.444, F.445, V.449, L.450 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.150, B:F.197 Hydrogen bonds: B:H.193, B:S.200, B:S.200, B:R.202, B:W.302, B:W.302, B:H.304, B:H.304, B:G.305, B:T.444 Salt bridges: B:R.202, B:K.236, B:H.304, B:H.304 pi-Stacking: B:F.197, B:F.445 pi-Cation interactions: B:R.202, B:R.202 NDP.6: 18 residues within 4Å: Chain C: P.150, H.193, F.197, S.200, R.202, D.212, Y.214, H.234, K.236, V.301, W.302, P.303, H.304, Q.441, T.444, F.445, V.449, L.450 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:P.150 Hydrogen bonds: C:H.193, C:S.200, C:Y.214, C:W.302, C:H.304, C:H.304 Salt bridges: C:R.202, C:K.236, C:H.304, C:H.304 pi-Stacking: C:F.197, C:F.445 pi-Cation interactions: C:R.202, C:R.202 NDP.8: 18 residues within 4Å: Chain D: P.150, H.193, F.197, S.200, R.202, D.212, Y.214, H.234, K.236, V.301, W.302, P.303, H.304, Q.441, T.444, F.445, V.449, L.450 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:P.150 Hydrogen bonds: D:H.193, D:S.200, D:S.200, D:R.202, D:Y.214, D:W.302, D:W.302, D:H.304, D:T.444 Water bridges: D:G.305 Salt bridges: D:R.202, D:K.236, D:H.304, D:H.304 pi-Stacking: D:F.197 pi-Cation interactions: D:R.202, D:R.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ko, T.P. et al., Structure of orthorhombic crystals of beef liver catalase. Acta Crystallogr.,Sect.D (1999)

Release Date

1998-10-14

Peptides

PROTEIN (CATALASE): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PROTEIN (CATALASE)

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