SMTL ID : 5yby.1

Structure of human Gliomedin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: F.118, N.126, N.174, A.175, L.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.126, A:N.126, A:A.175, A:L.220 NA.2: 4 residues within 4Å: Chain A: M.190, D.209, R.211, T.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.190 NA.3: 5 residues within 4Å: Chain A: V.16, V.37, E.39, K.47, F.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.39, A:K.47 NA.4: 6 residues within 4Å: Chain A: K.188, D.189, R.211, Q.214, S.215, V.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.188, A:R.211 Water bridges: A:L.217

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

NAG.5: 8 residues within 4Å: Chain A: N.108, S.140, V.142, D.143, S.146, L.148, N.164, T.166 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.148 Hydrogen bonds: A:S.140, A:D.143 Water bridges: A:N.164 NAG.6: 3 residues within 4Å: Chain A: Y.77, N.78, E.154 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.154, A:E.154 NAG.7: 2 residues within 4Å: Chain A: N.57, S.59 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 1 residues within 4Å: Chain A: S.31 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.31

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 6 residues within 4Å: Chain A: Y.116, A.119, K.169, S.170 Ligands: CA.11, CA.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.169 Water bridges: A:Y.116, A:A.119, A:S.170, A:S.170 EDO.10: 7 residues within 4Å: Chain A: H.70, F.112, D.113, R.114, Y.116, K.122, Y.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.124 Water bridges: A:Y.116, A:K.122

2 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.11: 3 residues within 4Å: Chain A: K.115, K.169 Ligands: EDO.9 No protein-ligand interaction detected (PLIP) CA.12: 2 residues within 4Å: Chain A: S.170 Ligands: EDO.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., High resolution structure of human gliomedin. To Be Published

Release Date

2018-10-03

Peptides

Gliomedin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Gliomedin