This entry has been superseded by
8Y9X
on March 13, 2024, midnight.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- monomer
- Ligands
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 10 x IOD: IODIDE ION(Non-functional Binders)
IOD.3: 2 residues within 4Å:- Chain A: N.197, P.262
Ligand excluded by PLIPIOD.4: 2 residues within 4Å:- Chain A: P.353, P.541
Ligand excluded by PLIPIOD.5: 3 residues within 4Å:- Chain A: N.333, Q.334, F.346
Ligand excluded by PLIPIOD.6: 2 residues within 4Å:- Chain A: F.426, W.647
Ligand excluded by PLIPIOD.7: 4 residues within 4Å:- Chain A: E.480, R.514, I.676, T.677
Ligand excluded by PLIPIOD.8: 3 residues within 4Å:- Chain A: N.212, R.213, R.623
Ligand excluded by PLIPIOD.9: 3 residues within 4Å:- Chain A: K.579, G.583
- Ligands: PEG.20
Ligand excluded by PLIPIOD.10: 2 residues within 4Å:- Chain A: L.341, A.342
Ligand excluded by PLIPIOD.13: 2 residues within 4Å:- Chain A: S.315, R.319
Ligand excluded by PLIPIOD.32: 6 residues within 4Å:- Chain A: A.161, R.162, W.163, N.458, V.459, W.569
Ligand excluded by PLIP- 1 x BR: BROMIDE ION(Non-covalent)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 5 x SCN: THIOCYANATE ION(Non-functional Binders)
SCN.14: 5 residues within 4Å:- Chain A: N.347, K.349, P.351, P.353, C.365
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.349
SCN.22: 3 residues within 4Å:- Chain A: T.140, I.141
- Ligands: PEG.19
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:I.141
SCN.23: 3 residues within 4Å:- Chain A: R.570, L.575, P.626
1 PLIP interactions:1 interactions with chain A- Water bridges: A:R.570
SCN.24: 4 residues within 4Å:- Chain A: S.476, L.478, P.484, K.519
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.519
SCN.25: 2 residues within 4Å:- Chain A: H.494, H.546
No protein-ligand interaction detected (PLIP)- 7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.15: 6 residues within 4Å:- Chain A: R.193, N.197, P.266, K.267, R.535, N.536
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:R.193, A:N.197, A:K.267, A:K.267, A:R.535, A:R.535, A:N.536
PEG.16: 4 residues within 4Å:- Chain A: R.149, L.153, N.450, S.451
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.149, A:N.450
PEG.17: 3 residues within 4Å:- Chain A: R.362, I.504, K.505
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.362, A:K.505
PEG.18: 5 residues within 4Å:- Chain A: N.333, Q.334, A.336, W.337, A.342
No protein-ligand interaction detected (PLIP)PEG.19: 5 residues within 4Å:- Chain A: P.314, S.318, R.321, L.323
- Ligands: SCN.22
1 PLIP interactions:1 interactions with chain A- Water bridges: A:R.321
PEG.20: 5 residues within 4Å:- Chain A: S.576, P.578, T.586, V.587
- Ligands: IOD.9
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.576
- Water bridges: A:S.576
PEG.21: 3 residues within 4Å:- Chain A: K.589, P.617, M.618
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.589
- 6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)(Non-functional Binders)
NAG.26: 4 residues within 4Å:- Chain A: N.212, R.213, I.432, Q.685
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.213
NAG.27: 5 residues within 4Å:- Chain A: N.358, A.361, W.501, K.505
- Ligands: NAG.28
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.358, A:A.361
NAG.28: 2 residues within 4Å:- Chain A: E.488
- Ligands: NAG.27
1 PLIP interactions:1 interactions with chain A- Water bridges: A:K.505
NAG.29: 3 residues within 4Å:- Chain A: N.449, S.451, V.452
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.449
- Water bridges: A:S.451, A:D.453
NAG.30: 8 residues within 4Å:- Chain A: N.322, S.325, L.327, L.329, A.331, V.332, Q.334
- Ligands: NAG.31
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:N.322, A:S.325, A:V.332, A:Q.334, A:Q.334
NAG.31: 1 residues within 4Å:- Ligands: NAG.30
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Viswanathan, V. et al., Structural evidence for the order of preference of inorganic substrates in mammalian heme peroxidases: crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl. To Be Published
- Release Date
- 2023-08-16
- Peptides
- Lactoperoxidase: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A