SMTL ID : 6dy1.1

Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) with fatty acid (myristate), in presence of Triton X-100

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 8 residues within 4Å: Chain A: L.17, F.18, N.19 Chain B: Q.35, L.37, G.40, Q.41, I.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.40 NAG.2: 2 residues within 4Å: Chain A: R.43, N.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.89 NAG.7: 6 residues within 4Å: Chain B: V.203, Y.206, N.207, N.208, P.231, S.232 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.206 Hydrogen bonds: B:N.208, B:S.232 Water bridges: B:N.208

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

SO4.3: 2 residues within 4Å: Chain A: P.32, R.35 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.35 SO4.8: 3 residues within 4Å: Chain B: Y.206, R.229, N.230 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.206, B:Y.206, B:N.230 Salt bridges: B:R.229 SO4.9: 4 residues within 4Å: Chain A: Q.48 Chain B: Y.23, G.24, S.25 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.23, B:G.24, B:S.25, B:S.25, B:S.25, A:Q.48 SO4.10: 7 residues within 4Å: Chain B: E.78, D.120, N.139, R.140, D.141 Ligands: SO4.11, CL.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.78, B:R.140 Salt bridges: B:R.140 SO4.11: 8 residues within 4Å: Chain B: E.78, V.81, A.82, L.86, H.88, R.140, D.141 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.78, B:E.78, B:D.141 Salt bridges: B:H.88

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.35, H.36 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: E.160, T.161, N.162, Y.163, R.176 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: A.102, E.103, A.107, R.111 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: R.227 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: D.20, R.175, N.207 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: R.71, D.72, R.73, Y.163 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: R.73, G.74 Ligands: SO4.10 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: G.142, P.143 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: R.96, T.97, S.100 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: H.62, T.128, A.219 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain A: P.13 Chain B: R.227 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: Y.110, R.111, K.114, T.115 Ligand excluded by PLIP

2 x TON: 2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL(Non-covalent)

TON.5: 13 residues within 4Å: Chain A: I.62, L.69, L.97, L.100, E.103, Y.104, F.107 Chain B: W.76, N.79, L.80, A.83, L.84, I.118 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.80, B:A.83, B:L.84, A:L.69, A:L.97 TON.6: 7 residues within 4Å: Chain A: A.25, E.27, L.28, L.31, R.82, G.83, D.86 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.27, A:L.28, A:L.28, A:L.31, A:D.86

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.23: 18 residues within 4Å: Chain A: V.42, A.45, V.46, V.49, V.98, A.101, Y.102 Chain B: C.1, L.19, Y.21, L.27, L.30, F.49, I.50, G.51, Y.52, W.56, E.70 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.21, B:Y.21, B:L.27, B:L.30, B:Y.52, B:Y.52, B:W.56 Hydrogen bonds: B:E.70, B:E.70, B:E.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., Molecular mechanism of activation of the immunoregulatory amidase NAAA. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-09-26

Peptides

N-acylethanolamine acid amidase alpha-subunit: A
N-acylethanolamine acid amidase beta-subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acylethanolamine acid amidase alpha-subunit

N-acylethanolamine acid amidase beta-subunit

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