SMTL ID : 4enz.1

Structure of human ceruloplasmin at 2.6 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: N.138, I.1035 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.138 NAG.11: 4 residues within 4Å: Chain A: S.388, G.389, I.390, N.397 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.390

6 x CU: COPPER (II) ION(Non-covalent)

CU.2: 5 residues within 4Å: Chain A: V.294, H.295, C.338, H.343, L.348 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.295, A:C.338, A:H.343 CU.3: 4 residues within 4Å: Chain A: H.182, H.999, H.1039 Ligands: OXY.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.182, A:H.999, A:H.1039 CU.4: 6 residues within 4Å: Chain A: H.120, H.122, H.997, H.999 Ligands: O.8, OXY.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.120, A:H.997 CU.5: 4 residues within 4Å: Chain A: H.122, H.180, H.1041 Ligands: OXY.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.122, A:H.180, A:H.1041 CU.6: 5 residues within 4Å: Chain A: H.656, C.699, T.701, H.704, M.709 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.656, A:C.699, A:H.704 CU.7: 6 residues within 4Å: Chain A: L.993, H.994, C.1040, V.1042, H.1045, M.1050 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.994, A:C.1040, A:H.1045

1 x O: OXYGEN ATOM(Non-covalent)

O.8: 7 residues within 4Å: Chain A: H.120, S.121, H.122, Y.126, H.997, G.1000 Ligands: CU.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.122, A:G.1000 Water bridges: A:H.1001

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.9: 11 residues within 4Å: Chain A: H.120, H.122, H.180, H.182, H.997, H.999, H.1039, H.1041 Ligands: CU.3, CU.4, CU.5 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: K.128, Q.143, D.146, D.147 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.128, A:Q.143, A:D.146, A:D.147, H2O.2

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 5 residues within 4Å: Chain A: Y.55, G.64, Y.67, S.256, N.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.64, A:Y.67

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: Y.665, W.667, R.672, T.674, A.675, N.676, L.683 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.665, A:N.676, A:N.676

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samygina, V.R. et al., Ceruloplasmin: macromolecular assemblies with iron-containing acute phase proteins. Plos One (2013)

Release Date

2013-04-17

Peptides

Ceruloplasmin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ceruloplasmin