SMTL ID : 1dgb.1

HUMAN ERYTHROCYTE CATALASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 24 residues within 4Å: Chain A: R.69, V.70, V.71, H.72, R.109, G.128, V.143, G.144, N.145, F.158, G.213, S.214, H.215, L.296, F.331, M.347, R.351, A.354, Y.355, T.358, H.359, R.362 Chain C: M.58, D.62 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:V.70, A:V.71, A:H.72, A:V.143, A:F.158, A:F.158, A:F.158, A:F.158, A:L.296, A:R.351, A:A.354, A:Y.355, A:Y.355, A:T.358 Water bridges: A:V.70, A:T.358, A:R.362, A:R.362 Salt bridges: A:R.69, A:R.69, A:R.109, A:H.359, A:R.362 pi-Stacking: A:H.72, A:F.158 pi-Cation interactions: A:R.351, A:R.351 Metal complexes: A:Y.355 HEM.3: 26 residues within 4Å: Chain B: R.69, V.70, V.71, H.72, R.109, G.128, F.129, V.143, G.144, N.145, P.155, F.158, G.213, S.214, H.215, L.296, F.331, M.347, R.351, A.354, Y.355, T.358, H.359, R.362 Chain D: M.58, D.62 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:V.71, B:H.72, B:V.143, B:N.145, B:F.158, B:F.158, B:F.158, B:F.158, B:L.296, B:R.351, B:A.354, B:Y.355 Water bridges: B:V.70, B:I.329, B:R.362 Salt bridges: B:R.69, B:R.69, B:R.109, B:H.359, B:R.362 pi-Stacking: B:H.72, B:F.158 pi-Cation interactions: B:R.351 Metal complexes: B:Y.355 HEM.4: 25 residues within 4Å: Chain A: M.58, D.62 Chain C: R.69, V.70, V.71, H.72, R.109, G.128, F.129, V.143, G.144, N.145, P.155, F.158, G.213, S.214, H.215, L.296, F.331, M.347, R.351, Y.355, T.358, H.359, R.362 26 PLIP interactions: 26 interactions with chain C, Hydrophobic interactions: C:V.70, C:V.71, C:H.72, C:V.143, C:N.145, C:P.155, C:F.158, C:F.158, C:F.158, C:F.158, C:L.296, C:R.351, C:Y.355 Hydrogen bonds: C:T.358 Water bridges: C:V.70, C:I.329 Salt bridges: C:R.69, C:R.69, C:R.109, C:H.359, C:R.362 pi-Stacking: C:H.72, C:F.158 pi-Cation interactions: C:R.351, C:R.351 Metal complexes: C:Y.355 HEM.6: 26 residues within 4Å: Chain B: M.58 Chain D: R.69, V.70, V.71, H.72, R.109, G.128, F.129, V.143, G.144, N.145, F.150, P.155, F.158, G.213, S.214, H.215, L.296, F.331, M.347, R.351, A.354, Y.355, T.358, H.359, R.362 30 PLIP interactions: 30 interactions with chain D, Hydrophobic interactions: D:V.70, D:H.72, D:V.143, D:N.145, D:F.150, D:P.155, D:F.158, D:F.158, D:F.158, D:L.296, D:F.331, D:R.351, D:A.354, D:Y.355, D:Y.355, D:Y.355 Water bridges: D:A.130, D:I.329, D:T.358, D:T.358, D:R.362 Salt bridges: D:R.69, D:R.69, D:R.109, D:H.359, D:R.362 pi-Stacking: D:H.72, D:F.158 pi-Cation interactions: D:R.351 Metal complexes: D:Y.355

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

NDP.2: 15 residues within 4Å: Chain A: P.148, H.191, F.195, S.198, R.200, N.210, H.232, K.234, V.299, W.300, P.301, H.302, Q.439, F.443, V.447 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.148 Hydrogen bonds: A:H.191, A:S.198, A:S.198, A:N.210, A:Q.279, A:W.300, A:H.302 Water bridges: A:K.234, A:W.300, A:W.300, A:K.303 Salt bridges: A:R.200, A:K.234, A:H.302, A:H.302 pi-Stacking: A:F.443 pi-Cation interactions: A:R.200 NDP.5: 16 residues within 4Å: Chain C: P.148, H.191, F.195, S.198, R.200, N.210, H.232, K.234, I.239, V.299, W.300, P.301, H.302, Q.439, F.443, V.447 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:P.148 Hydrogen bonds: C:H.191, C:S.198, C:S.198, C:R.200, C:N.210, C:W.300, C:W.300, C:H.302 Water bridges: C:R.200, C:R.200, C:Y.212, C:Y.212, C:Q.279 Salt bridges: C:R.200, C:K.234, C:H.302, C:H.302 pi-Stacking: C:F.443 pi-Cation interactions: C:R.200, C:R.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Putnam, C.D. et al., Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism. J.Mol.Biol. (2000)

Release Date

2000-02-11

Peptides

CATALASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CATALASE

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