SMTL ID : 1dgg.1

HUMAN ERYTHROCYTE CATALSE CYANIDE COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x CYN: CYANIDE ION(Non-covalent)

CYN.1: 5 residues within 4Å: Chain A: V.70, H.71, F.157, Y.354 Ligands: HEM.2 No protein-ligand interaction detected (PLIP) CYN.4: 5 residues within 4Å: Chain B: V.70, H.71, F.157, Y.354 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) CYN.6: 5 residues within 4Å: Chain C: V.70, H.71, F.157, Y.354 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) CYN.9: 5 residues within 4Å: Chain D: V.70, H.71, F.157, Y.354 Ligands: HEM.10 No protein-ligand interaction detected (PLIP)

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 27 residues within 4Å: Chain A: R.68, V.69, V.70, H.71, R.108, G.127, F.128, V.142, G.143, N.144, F.149, P.154, F.157, G.212, S.213, H.214, L.295, F.330, M.346, R.350, Y.354, T.357, H.358, R.361 Chain C: M.57, D.61 Ligands: CYN.1 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:V.69, A:V.70, A:H.71, A:V.142, A:N.144, A:F.149, A:P.154, A:F.157, A:F.157, A:F.157, A:F.157, A:L.295, A:F.330, A:Y.354 Hydrogen bonds: A:T.357 Water bridges: A:V.69, A:I.328, A:R.361 Salt bridges: A:R.68, A:R.68, A:R.108, A:H.358, A:R.361 pi-Stacking: A:H.71, A:F.157 pi-Cation interactions: A:R.350 Metal complexes: A:Y.354 HEM.5: 28 residues within 4Å: Chain B: R.68, V.69, V.70, H.71, R.108, G.127, F.128, V.142, G.143, N.144, F.149, P.154, F.157, G.212, S.213, H.214, L.295, F.330, M.346, R.350, A.353, Y.354, T.357, H.358, R.361 Chain D: M.57, D.61 Ligands: CYN.4 27 PLIP interactions: 27 interactions with chain B, Hydrophobic interactions: B:V.69, B:V.70, B:H.71, B:V.142, B:N.144, B:F.149, B:P.154, B:F.157, B:F.157, B:F.157, B:L.295, B:R.350, B:A.353, B:Y.354 Water bridges: B:V.69, B:A.129, B:I.328, B:T.357 Salt bridges: B:R.68, B:R.68, B:R.108, B:H.358, B:R.361 pi-Stacking: B:H.71, B:F.157 pi-Cation interactions: B:R.350 Metal complexes: B:Y.354 HEM.7: 27 residues within 4Å: Chain A: M.57, D.61 Chain C: R.68, V.69, V.70, H.71, R.108, G.127, F.128, V.142, G.143, N.144, F.149, P.154, F.157, G.212, S.213, L.295, F.330, M.346, R.350, A.353, Y.354, T.357, H.358, R.361 Ligands: CYN.6 26 PLIP interactions: 26 interactions with chain C, Hydrophobic interactions: C:V.69, C:V.70, C:H.71, C:V.142, C:F.149, C:P.154, C:F.157, C:F.157, C:F.157, C:F.157, C:L.295, C:R.350, C:A.353, C:Y.354, C:Y.354 Water bridges: C:V.69, C:T.357 Salt bridges: C:R.68, C:R.68, C:R.108, C:H.358, C:R.361 pi-Stacking: C:H.71, C:F.157 pi-Cation interactions: C:R.350 Metal complexes: C:Y.354 HEM.10: 27 residues within 4Å: Chain B: M.57, D.61 Chain D: R.68, V.69, V.70, H.71, R.108, G.127, F.128, V.142, G.143, N.144, P.154, F.157, G.212, S.213, H.214, L.295, F.330, M.346, R.350, A.353, Y.354, T.357, H.358, R.361 Ligands: CYN.9 30 PLIP interactions: 30 interactions with chain D, Hydrophobic interactions: D:V.69, D:V.70, D:H.71, D:V.142, D:N.144, D:P.154, D:F.157, D:F.157, D:F.157, D:F.157, D:L.295, D:F.330, D:R.350, D:A.353, D:Y.354, D:Y.354, D:T.357 Water bridges: D:I.328, D:T.357, D:T.357, D:R.361 Salt bridges: D:R.68, D:R.68, D:R.108, D:H.358, D:R.361 pi-Stacking: D:H.71, D:F.157 pi-Cation interactions: D:R.350 Metal complexes: D:Y.354

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

NDP.3: 16 residues within 4Å: Chain A: P.147, H.190, F.194, S.197, R.199, N.209, H.231, K.233, V.298, W.299, P.300, H.301, Q.438, A.441, F.442, V.446 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.147, A:F.194 Hydrogen bonds: A:H.190, A:S.197, A:S.197, A:N.209, A:W.299, A:H.301 Water bridges: A:R.199, A:K.233, A:Q.278, A:W.299, A:K.302 Salt bridges: A:R.199, A:K.233, A:H.301, A:H.301 pi-Stacking: A:F.194, A:F.442 pi-Cation interactions: A:R.199 NDP.8: 17 residues within 4Å: Chain C: P.147, H.190, F.194, S.197, R.199, N.209, H.231, K.233, I.238, V.298, W.299, P.300, H.301, Q.438, F.442, V.446, L.447 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.147 Hydrogen bonds: C:H.190, C:S.197, C:S.197, C:R.199, C:N.209, C:W.299, C:H.301, C:H.301 Water bridges: C:D.198, C:Y.211, C:Y.211, C:Q.278 Salt bridges: C:R.199, C:K.233, C:H.301, C:H.301 pi-Stacking: C:F.442 pi-Cation interactions: C:R.199

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

2000-02-17

Peptides

CATALASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CATALASE

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