- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.98 Å
- Oligo State
- monomer
- Ligands
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x NO: NITRIC OXIDE(Non-covalent)
NO.5: 6 residues within 4Å:- Chain A: Q.105, H.109, H.351
- Ligands: NO2.6, IOD.18, HEM.27
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.105, A:H.351
- Water bridges: A:R.255
NO.31: 5 residues within 4Å:- Chain A: S.254, R.255, F.381
- Ligands: NO2.6, NA.38
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.254
- 1 x NO2: NITRITE ION(Non-covalent)
- 7 x NO3: NITRATE ION(Non-functional Binders)
NO3.7: 5 residues within 4Å:- Chain A: N.95, R.96, R.504, R.506
- Ligands: NAG.2
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:R.506, A:R.506
NO3.8: 5 residues within 4Å:- Chain A: P.461, K.462, T.463, G.466
- Ligands: IOD.26
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.462, A:T.463, A:G.466
NO3.13: 8 residues within 4Å:- Chain A: E.363, Y.365, R.397, H.558, V.559, T.560, K.561
- Ligands: IOD.25
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.363, A:R.397, A:T.560, A:K.561
NO3.14: 3 residues within 4Å:- Chain A: P.197, S.198
- Ligands: IOD.23
No protein-ligand interaction detected (PLIP)NO3.15: 6 residues within 4Å:- Chain A: E.77, N.80, K.81, P.145, K.146
- Ligands: IOD.24
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.80
NO3.16: 7 residues within 4Å:- Chain A: V.215, N.216, Q.217, E.218, P.228, F.229
- Ligands: IOD.22
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:N.216, A:Q.217, A:E.218, A:E.218, A:F.229
NO3.17: 3 residues within 4Å:- Chain A: K.65, T.66
- Ligands: SCN.9
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.65, A:T.66
- 4 x SCN: THIOCYANATE ION(Non-functional Binders)
SCN.9: 3 residues within 4Å:- Chain A: T.66, N.68
- Ligands: NO3.17
No protein-ligand interaction detected (PLIP)SCN.10: 4 residues within 4Å:- Chain A: S.359, L.361, P.367, K.402
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.402
SCN.12: 4 residues within 4Å:- Chain A: R.76, P.149, K.150, N.419
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.150
- Water bridges: A:T.153
SCN.32: 5 residues within 4Å:- Chain A: H.565, A.566, F.567, Q.568
- Ligands: NAG.2
No protein-ligand interaction detected (PLIP)- 3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.11: 5 residues within 4Å:- Chain A: N.230, P.236, C.248, S.254, F.381
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.230
- Water bridges: A:S.254
EDO.28: 7 residues within 4Å:- Chain A: E.218, A.219, F.229, H.245, V.246, I.387, K.388
No protein-ligand interaction detected (PLIP)EDO.30: 2 residues within 4Å:- Chain A: E.538, R.541
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.538, A:R.541
- 13 x IOD: IODIDE ION(Non-functional Binders)
IOD.18: 7 residues within 4Å:- Chain A: H.109, R.255, E.258
- Ligands: NO.5, NO2.6, HEM.27, NA.38
Ligand excluded by PLIPIOD.19: 2 residues within 4Å:- Chain A: P.236, T.425
Ligand excluded by PLIPIOD.20: 4 residues within 4Å:- Chain A: Q.409, N.410, N.473, K.479
Ligand excluded by PLIPIOD.21: 5 residues within 4Å:- Chain A: R.45, W.46, N.341, V.342, W.452
Ligand excluded by PLIPIOD.22: 4 residues within 4Å:- Chain A: Q.217, E.218, F.229
- Ligands: NO3.16
Ligand excluded by PLIPIOD.23: 3 residues within 4Å:- Chain A: P.197, S.198
- Ligands: NO3.14
Ligand excluded by PLIPIOD.24: 3 residues within 4Å:- Chain A: N.80, P.145
- Ligands: NO3.15
Ligand excluded by PLIPIOD.25: 5 residues within 4Å:- Chain A: E.363, R.397, T.560, K.561
- Ligands: NO3.13
Ligand excluded by PLIPIOD.26: 4 residues within 4Å:- Chain A: K.462, T.463, G.466
- Ligands: NO3.8
Ligand excluded by PLIPIOD.34: 2 residues within 4Å:- Chain A: F.309, W.530
Ligand excluded by PLIPIOD.35: 3 residues within 4Å:- Chain A: H.377
- Ligands: IOD.36, IOD.37
Ligand excluded by PLIPIOD.36: 3 residues within 4Å:- Chain A: H.377
- Ligands: IOD.35, IOD.37
Ligand excluded by PLIPIOD.37: 4 residues within 4Å:- Chain A: T.378, H.429
- Ligands: IOD.35, IOD.36
Ligand excluded by PLIP- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)
HEM.27: 25 residues within 4Å:- Chain A: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, R.255, E.258, Q.259, T.344, F.347, R.348, G.350, H.351, V.354, F.380, L.417, Q.423, L.433, I.436, R.440
- Ligands: NO.5, NO2.6, IOD.18
26 PLIP interactions:26 interactions with chain A,- Hydrophobic interactions: A:Q.105, A:Q.105, A:E.258, A:Q.259, A:F.347, A:F.347, A:R.348, A:V.354, A:V.354, A:F.380, A:L.417, A:L.433, A:L.433, A:I.436
- Hydrogen bonds: A:D.112, A:A.114
- Water bridges: A:A.114, A:R.255, A:R.348, A:R.348, A:R.348, A:R.348
- Salt bridges: A:R.255, A:R.348, A:R.440
- Metal complexes: A:H.351
- 1 x CA: CALCIUM ION(Non-covalent)
- 1 x OSM: 1-(OXIDOSULFANYL)METHANAMINE(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ahmad, M.I. et al., Structure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution. To be published
- Release Date
- 2023-04-05
- Peptides
- Lactoperoxidase: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.98 Å
- Oligo State
- monomer
- Ligands
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x NO: NITRIC OXIDE(Non-covalent)
- 1 x NO2: NITRITE ION(Non-covalent)
- 7 x NO3: NITRATE ION(Non-functional Binders)
- 4 x SCN: THIOCYANATE ION(Non-functional Binders)
- 3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 13 x IOD: IODIDE ION(Non-functional Binders)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 1 x OSM: 1-(OXIDOSULFANYL)METHANAMINE(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ahmad, M.I. et al., Structure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution. To be published
- Release Date
- 2023-04-05
- Peptides
- Lactoperoxidase: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A