- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.27 Å
- Oligo State
- monomer
- Ligands
- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x CA: CALCIUM ION(Non-covalent)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)
HEM.6: 24 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, L.433, I.436, R.440
- Ligands: IOD.7, SCN.26, PEO.28
25 PLIP interactions:25 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: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:D.112, A:A.114
- Water bridges: A:R.255, A:R.348, A:R.348
- Salt bridges: A:R.348, A:R.348, A:R.440
- Metal complexes: A:H.351
- 13 x IOD: IODIDE ION(Non-functional Binders)
IOD.7: 6 residues within 4Å:- Chain A: H.109, R.255, E.258
- Ligands: HEM.6, SCN.26, PEO.28
Ligand excluded by PLIPIOD.8: 2 residues within 4Å:- Chain A: F.381
- Ligands: SCN.26
Ligand excluded by PLIPIOD.9: 2 residues within 4Å:- Chain A: F.309, W.530
Ligand excluded by PLIPIOD.10: 1 residues within 4Å:- Chain A: S.359
Ligand excluded by PLIPIOD.11: 4 residues within 4Å:- Chain A: N.216, Q.217, E.218, F.229
Ligand excluded by PLIPIOD.12: 2 residues within 4Å:- Chain A: N.80, P.145
Ligand excluded by PLIPIOD.13: 6 residues within 4Å:- Chain A: A.44, R.45, W.46, N.341, V.342, W.452
Ligand excluded by PLIPIOD.14: 4 residues within 4Å:- Chain A: E.363, R.397, I.559, T.560
Ligand excluded by PLIPIOD.15: 2 residues within 4Å:- Chain A: P.236, P.424
Ligand excluded by PLIPIOD.16: 3 residues within 4Å:- Chain A: K.462, T.463, G.466
Ligand excluded by PLIPIOD.17: 3 residues within 4Å:- Chain A: H.565, A.566, F.567
Ligand excluded by PLIPIOD.18: 1 residues within 4Å:- Chain A: P.197
Ligand excluded by PLIPIOD.19: 4 residues within 4Å:- Chain A: P.159, F.160, S.161, H.426
Ligand excluded by PLIP- 4 x OSM: 1-(OXIDOSULFANYL)METHANAMINE(Non-covalent)
OSM.20: 3 residues within 4Å:- Chain A: H.377, T.378, H.429
2 PLIP interactions:2 interactions with chain A- Water bridges: A:H.377, A:T.378
OSM.21: 6 residues within 4Å:- Chain A: N.230, K.232, S.235, P.236, C.248
- Ligands: SCN.25
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.230, A:N.230, A:C.248
- Water bridges: A:K.232
OSM.22: 5 residues within 4Å:- Chain A: N.95, R.96, R.504, R.506
- Ligands: NAG.1
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.96, A:R.96, A:R.506, A:R.506
OSM.23: 3 residues within 4Å:- Chain A: S.198, L.199, R.202
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.202
- 4 x SCN: THIOCYANATE ION(Non-functional Binders)
SCN.24: 4 residues within 4Å:- Chain A: F.229, R.245, V.246, I.387
No protein-ligand interaction detected (PLIP)SCN.25: 8 residues within 4Å:- Chain A: P.236, C.248, A.254, R.255, A.256, S.257, F.381
- Ligands: OSM.21
No protein-ligand interaction detected (PLIP)SCN.26: 7 residues within 4Å:- Chain A: R.255, E.258, F.381
- Ligands: HEM.6, IOD.7, IOD.8, PEO.28
No protein-ligand interaction detected (PLIP)SCN.27: 3 residues within 4Å:- Chain A: E.373, L.374, P.375
No protein-ligand interaction detected (PLIP)- 1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Singh, P.K. et al., Crystal structure of yak lactoperoxidase at 2.27 A resolution. To Be Published
- Release Date
- 2019-10-16
- Peptides
- Lactoperoxidase: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.27 Å
- Oligo State
- monomer
- Ligands
- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x CA: CALCIUM ION(Non-covalent)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)
- 13 x IOD: IODIDE ION(Non-functional Binders)
- 4 x OSM: 1-(OXIDOSULFANYL)METHANAMINE(Non-covalent)
- 4 x SCN: THIOCYANATE ION(Non-functional Binders)
- 1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Singh, P.K. et al., Crystal structure of yak lactoperoxidase at 2.27 A resolution. To Be Published
- Release Date
- 2019-10-16
- Peptides
- Lactoperoxidase: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A