SMTL ID : 6nwx.1

Structure of mouse GILT, an enzyme involved in antigen processing

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: P.11, N.45 Ligands: 1PE.5, SO4.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 3 residues within 4Å: Chain B: P.11, N.45 Ligands: 1PE.12 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: N.58, G.61, W.63 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.63 Hydrogen bonds: A:N.58, A:G.61 NAG.11: 3 residues within 4Å: Chain B: N.58, G.61, W.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.61

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 7 residues within 4Å: Chain A: R.26, V.30, E.100, E.101, D.103 Chain B: E.90, L.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.101 Water bridges: A:E.101 1PE.5: 10 residues within 4Å: Chain A: W.37, M.41, E.42, M.44, I.46, L.84, K.89, E.90, F.93 Ligands: NAG-NAG-BMA.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.89 Water bridges: A:I.46, A:I.46, A:L.48 1PE.12: 10 residues within 4Å: Chain B: W.37, M.41, E.42, M.44, N.45, I.46, L.84, K.89, F.93 Ligands: NAG-NAG-BMA.2 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.89, B:K.89 1PE.13: 6 residues within 4Å: Chain A: E.90, L.94 Chain B: R.26, V.30, E.100, E.101 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.101

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

SO4.6: 4 residues within 4Å: Chain A: L.21, C.22, G.23, H.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.23 Water bridges: A:A.24 Salt bridges: A:H.69 SO4.7: 4 residues within 4Å: Chain A: S.9, G.181, T.182, E.183 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.9, A:Y.179, A:T.182, A:T.182, A:E.183 SO4.8: 2 residues within 4Å: Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) SO4.9: 3 residues within 4Å: Chain A: R.13, N.161, K.163 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.161 Water bridges: A:Q.180, A:Q.180 Salt bridges: A:R.13, A:K.163 SO4.10: 3 residues within 4Å: Chain A: E.127, G.131, K.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.127, A:K.132 SO4.14: 4 residues within 4Å: Chain B: S.9, G.181, T.182, E.183 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.9, B:T.182, B:T.182, B:E.183 Water bridges: B:S.9 SO4.15: 3 residues within 4Å: Chain B: R.13, N.161, K.163 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.161 Water bridges: B:K.163, B:K.163, B:K.163, B:Q.180, B:Q.180, B:Q.180, B:Q.180 Salt bridges: B:R.13, B:K.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cresswell, P., Gamma-interferon-inducible lysosomal thiol reductase (GILT). Maturation, activity, and mechanism of action. To Be Published

Release Date

2020-08-12

Peptides

Gamma-interferon-inducible lysosomal thiol reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gamma-interferon-inducible lysosomal thiol reductase