SMTL ID : 5gkn.1

Catalase structure determined by electron crystallography of thin 3D crystals

Coordinates

PDB Format Compare

Method

ELECTRON CRYSTALLOGRAPHY 3.20 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: R.72, V.73, V.74, H.75, R.112, G.131, V.146, G.147, N.148, A.158, F.161, S.217, H.218, L.299, F.334, M.350, R.354, A.357, Y.358, T.361, H.362, R.365 Chain D: M.61, D.65 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:V.73, A:H.75, A:V.146, A:A.158, A:F.161, A:F.161, A:F.161, A:F.161, A:L.299, A:A.357, A:Y.358, A:Y.358 Water bridges: A:R.112, A:S.114, A:T.361, A:T.361 Salt bridges: A:R.72, A:R.72, A:R.112, A:H.362, A:R.365 pi-Stacking: A:H.75, A:F.161 pi-Cation interactions: A:R.354 Metal complexes: A:Y.358 HEM.3: 24 residues within 4Å: Chain B: R.72, V.73, V.74, H.75, R.112, G.131, A.133, V.146, G.147, N.148, A.158, F.161, S.217, L.299, F.334, M.350, R.354, A.357, Y.358, T.361, H.362, R.365 Chain C: M.61, D.65 25 PLIP interactions: 25 interactions with chain B, Hydrophobic interactions: B:V.73, B:H.75, B:V.146, B:N.148, B:A.158, B:F.161, B:F.161, B:F.161, B:F.161, B:L.299, B:R.354, B:A.357, B:Y.358 Hydrogen bonds: B:T.361 Water bridges: B:L.332 Salt bridges: B:R.72, B:R.72, B:R.112, B:H.362, B:R.365 pi-Stacking: B:H.75, B:F.153, B:F.161 pi-Cation interactions: B:R.354 Metal complexes: B:Y.358 HEM.5: 21 residues within 4Å: Chain B: M.61, D.65 Chain C: R.72, V.73, V.74, H.75, R.112, G.131, V.146, G.147, N.148, F.161, H.218, L.299, F.334, M.350, R.354, Y.358, T.361, H.362, R.365 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:V.73, C:H.75, C:V.146, C:F.161, C:F.161, C:F.161, C:F.161, C:L.299, C:M.350, C:R.354, C:Y.358 Salt bridges: C:R.72, C:R.72, C:R.112, C:H.362, C:R.365 pi-Stacking: C:H.75, C:F.161 pi-Cation interactions: C:R.354 Metal complexes: C:Y.358 HEM.7: 26 residues within 4Å: Chain A: M.61, D.65 Chain D: R.72, V.73, V.74, H.75, R.112, G.131, F.132, V.146, G.147, N.148, A.158, F.161, G.216, S.217, H.218, L.299, L.332, F.334, M.350, R.354, Y.358, T.361, H.362, R.365 24 PLIP interactions: 24 interactions with chain D, Hydrophobic interactions: D:V.73, D:V.74, D:H.75, D:V.146, D:A.158, D:F.161, D:F.161, D:F.161, D:F.161, D:F.161, D:L.299, D:R.354, D:Y.358 Water bridges: D:V.73, D:T.361 Salt bridges: D:R.72, D:R.72, D:R.112, D:H.362, D:R.365 pi-Stacking: D:H.75, D:F.161 pi-Cation interactions: D:R.354 Metal complexes: D:Y.358

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

NDP.2: 17 residues within 4Å: Chain A: P.151, H.194, F.198, S.201, R.203, N.213, Y.215, H.235, K.237, V.302, W.303, P.304, H.305, Q.442, T.445, F.446, V.450 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.151 Hydrogen bonds: A:H.194, A:S.201, A:S.201, A:N.213, A:W.303, A:H.305, A:H.305 Water bridges: A:K.237, A:H.305 Salt bridges: A:R.203, A:K.237, A:H.305, A:H.305 pi-Stacking: A:F.446 pi-Cation interactions: A:R.203, A:R.203 NDP.4: 17 residues within 4Å: Chain B: P.151, H.194, F.198, S.201, R.203, N.213, H.235, K.237, I.242, V.302, W.303, P.304, H.305, Q.442, T.445, F.446, V.450 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.151 Hydrogen bonds: B:H.194, B:S.201, B:S.201, B:N.213, B:K.237, B:W.303, B:H.305, B:F.446 Salt bridges: B:R.203, B:K.237, B:H.305, B:H.305 pi-Stacking: B:F.446 pi-Cation interactions: B:R.203, B:R.203 NDP.6: 15 residues within 4Å: Chain C: H.194, F.198, S.201, R.203, N.213, H.235, K.237, V.302, W.303, P.304, H.305, Q.442, T.445, F.446, V.450 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:H.194, C:S.201, C:S.201, C:N.213, C:K.237, C:W.303, C:H.305, C:F.446 Salt bridges: C:R.203, C:K.237, C:H.305, C:H.305 pi-Stacking: C:F.446 pi-Cation interactions: C:R.203, C:R.203 NDP.8: 18 residues within 4Å: Chain D: P.151, H.194, F.198, S.201, R.203, N.213, H.235, K.237, I.242, V.302, W.303, P.304, H.305, Q.442, T.445, F.446, V.450, L.451 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:P.151, D:V.302 Hydrogen bonds: D:H.194, D:N.213, D:K.237, D:W.303, D:H.305, D:H.305, D:F.446 Water bridges: D:G.306, D:G.306 Salt bridges: D:R.203, D:K.237, D:H.305, D:H.305 pi-Stacking: D:F.446 pi-Cation interactions: D:R.203, D:R.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yonekura, K. et al., Refinement of Cryo-EM Structures Using Scattering Factors of Charged Atoms. J.Appl.Crystallogr. (2016)

Release Date

2016-10-26

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase

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