SMTL ID : 6slf.1

Nalpha-acylglutamine aminoacylase from Corynebacterium sp.releasing human axilla odorants co-crystallised with high affinity inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: D.80, C.106, H.108, E.141, E.142, H.169 Ligands: ZN.2, LJ8.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.106, A:H.108, A:H.169, H2O.1 ZN.2: 5 residues within 4Å: Chain A: C.106, E.142, H.371 Ligands: ZN.1, LJ8.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.106, A:E.142, A:E.142, A:H.371 ZN.6: 5 residues within 4Å: Chain B: C.106, E.142, H.371 Ligands: ZN.7, LJ8.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.106, B:E.142, B:E.142, B:H.371 ZN.7: 7 residues within 4Å: Chain B: C.106, H.108, E.141, E.142, H.169 Ligands: ZN.6, LJ8.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.106, B:H.108, B:H.169, H2O.12 ZN.12: 5 residues within 4Å: Chain C: C.106, E.142, H.371 Ligands: ZN.13, LJ8.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.106, C:E.142, C:E.142, C:H.371 ZN.13: 7 residues within 4Å: Chain C: C.106, H.108, E.141, E.142, H.169 Ligands: ZN.12, LJ8.14 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.106, C:H.108, C:H.169, H2O.22 ZN.16: 5 residues within 4Å: Chain D: C.106, E.142, H.371 Ligands: ZN.17, LJ8.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.106, D:E.142, D:E.142, D:H.371 ZN.17: 7 residues within 4Å: Chain D: C.106, H.108, E.141, E.142, H.169 Ligands: ZN.16, LJ8.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.106, D:H.108, D:H.169, H2O.33

4 x LJ8: (2~{S})-5-azanyl-2-[[[(3~{S})-3-methyl-5-phenyl-pentyl]-oxidanyl-phosphoryl]methyl]-5-oxidanylidene-pentanoic acid(Non-covalent)

LJ8.3: 24 residues within 4Å: Chain A: C.106, H.108, E.141, E.142, G.143, H.169, F.171, A.190, N.192, R.265, D.302, V.304, L.336, G.338, S.339, E.340, N.370, H.371 Chain B: H.203, S.205, R.206, N.252 Ligands: ZN.1, ZN.2 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:R.206, A:F.171, A:L.336, A:L.336 Hydrogen bonds: B:N.252, A:E.142, A:G.143, A:N.192, A:D.302, A:S.339 Salt bridges: B:H.203, A:R.265 pi-Stacking: B:H.203 Water bridges: A:G.144 LJ8.8: 24 residues within 4Å: Chain A: H.203, S.205, R.206, N.252 Chain B: C.106, H.108, E.141, E.142, G.143, H.169, F.171, A.190, N.192, R.265, D.302, V.304, L.336, G.338, S.339, E.340, N.370, H.371 Ligands: ZN.6, ZN.7 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:R.206, B:F.171, B:L.336, B:L.336 Hydrogen bonds: A:N.252, B:E.142, B:G.143, B:N.192, B:D.302, B:D.302, B:S.339 Salt bridges: A:H.203, B:R.265 pi-Stacking: A:H.203 Water bridges: B:G.144 LJ8.14: 24 residues within 4Å: Chain C: C.106, H.108, E.141, E.142, G.143, H.169, F.171, A.190, N.192, R.265, D.302, V.304, L.336, S.337, G.338, S.339, N.370, H.371 Chain D: H.203, S.205, R.206, N.252 Ligands: ZN.12, ZN.13 13 PLIP interactions: 4 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:R.206, C:F.171, C:L.336, C:L.336 Hydrogen bonds: D:N.252, C:G.143, C:N.192, C:D.302, C:S.339 Salt bridges: D:H.203, C:R.265 pi-Stacking: D:H.203 Water bridges: C:G.144 LJ8.18: 24 residues within 4Å: Chain C: H.203, S.205, R.206, N.252 Chain D: C.106, H.108, E.141, E.142, G.143, H.169, F.171, A.190, N.192, R.265, D.302, V.304, L.336, G.338, S.339, E.340, N.370, H.371 Ligands: ZN.16, ZN.17 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.171, D:L.336, D:L.336, C:R.206 Hydrogen bonds: D:G.143, D:N.192, D:D.302, D:D.302, D:S.339, C:N.252 Water bridges: D:G.144 Salt bridges: D:R.265, C:H.203 pi-Stacking: C:H.203

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: P.73, Q.316, P.396, W.397 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.316, A:Q.316 GOL.9: 11 residues within 4Å: Chain B: V.228, V.232, D.233, P.234, E.236, V.237, A.238 Chain C: V.228, P.234, E.236, A.238 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:E.236, C:A.238, B:V.232, B:A.238, B:A.238 GOL.10: 5 residues within 4Å: Chain B: W.193, E.273, Q.276, N.277, K.280 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.280, B:K.280

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

ACT.5: 6 residues within 4Å: Chain A: P.305, A.306, V.307, I.308, P.343, N.347 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.305, A:P.343 Hydrogen bonds: A:I.308, A:N.347, A:N.347 ACT.11: 6 residues within 4Å: Chain B: P.305, A.306, V.307, I.308, P.343, N.347 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.305, B:P.343 Hydrogen bonds: B:A.306, B:I.308, B:N.347 ACT.15: 6 residues within 4Å: Chain C: P.305, A.306, V.307, I.308, P.343, N.347 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:P.305, C:P.343 Hydrogen bonds: C:I.308, C:N.347 Water bridges: C:N.347 ACT.19: 6 residues within 4Å: Chain D: P.305, A.306, V.307, I.308, P.343, N.347 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.305, D:P.343 Hydrogen bonds: D:A.306, D:I.308

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.20: 14 residues within 4Å: Chain A: V.228, V.232, D.233, P.234, E.236, V.237, A.238 Chain D: V.228, V.232, D.233, P.234, E.236, V.237, A.238 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:V.232, A:A.238, A:A.238, D:V.228, D:A.238 Water bridges: A:E.236, D:N.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Natsch, A. et al., The specific biochemistry of human axilla odour formation viewed in an evolutionary context. Philos.Trans.R.Soc.Lond.B Biol.Sci. (2020)

Release Date

2020-03-11

Peptides

N-alpha-acyl-glutamine aminoacylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

N-alpha-acyl-glutamine aminoacylase