SMTL ID : 3pms.1

Recombinant peptide: N-glycanase F (PNGase F)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: P.141, D.142, Y.143, K.305 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.142, A:Y.143 Water bridges: A:K.107, A:K.107, A:K.107, A:D.142, A:D.142, A:K.184, A:K.305 Salt bridges: A:K.107, A:K.305 SO4.2: 1 residues within 4Å: Chain A: G.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.203 Water bridges: A:S.204

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: W.62, D.63, Y.88, W.210, N.246, R.251 Ligands: GOL.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.63, A:N.246, A:R.251 Water bridges: A:Y.88, A:N.246 GOL.4: 2 residues within 4Å: Chain A: T.35, N.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.35, A:T.35, A:N.113 GOL.5: 8 residues within 4Å: Chain A: P.163, Y.164, G.165, K.166, F.282, Q.283, N.284, W.285 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.164, A:Y.164, A:G.165, A:K.166, A:K.166, A:N.284, A:W.285 Water bridges: A:H.168, A:H.168 GOL.6: 5 residues within 4Å: Chain A: Q.177, L.178, P.179, T.180, S.311 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.177, A:L.178, A:T.180, A:S.311 Water bridges: A:T.180, A:S.311 GOL.7: 2 residues within 4Å: Chain A: L.232, M.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.232 GOL.8: 5 residues within 4Å: Chain A: T.140, P.141, D.142, K.144, N.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.141, A:K.144 GOL.9: 8 residues within 4Å: Chain A: D.63, R.64, E.121, W.123, S.158, I.159, W.194 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.64, A:R.64, A:S.158, A:W.194 GOL.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain A: N.11, K.13, K.51, R.97, D.133 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.11, A:K.13, A:K.51, A:K.51, A:R.97, A:D.133 Water bridges: A:R.97 GOL.12: 8 residues within 4Å: Chain A: D.63, Y.65, S.158, W.194, E.209, W.254 Ligands: GOL.3, GOL.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.63, A:S.158, A:S.158, A:E.209 Water bridges: A:Y.65, A:Y.65, A:E.209

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 4 residues within 4Å: Chain A: K.47, F.49, D.135, V.137 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.47 Hydrogen bonds: A:D.135 Water bridges: A:E.100 ACT.14: 3 residues within 4Å: Chain A: G.203, S.204, W.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.204 Salt bridges: A:R.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filitcheva, J. et al., Recombinant peptide:N-glycanase F (PNGase F). To be Published

Release Date

2011-01-26

Peptides

Peptide:N-glycosidase F: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptide:N-glycosidase F