SMTL ID : 6a0f.1 (1 other biounit)

Crystal structure of human protein N-terminal asparagine amidohydrolase (NTAN1) C75S mutant with Asn-Phe-Ala-Ala-Arg peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

1 x ASN- PHE- ALA- ALA: 5-mer peptide Asn-Phe-Ala-Ala-Arg(Non-covalent)

ASN-PHE-ALA-ALA.1: 16 residues within 4Å: Chain A: Q.51, D.71, T.73, T.74, S.75, H.92, A.205, T.208, L.209, N.252, L.253, S.254, T.255, E.260, H.267, I.268 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.208, A:L.209, A:L.209, A:I.268 Hydrogen bonds: A:Q.51, A:Q.51, A:Q.51, A:T.73, A:T.74, A:S.75, A:S.75, A:L.253, A:T.255, A:T.255 Water bridges: A:R.52, A:R.52

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: P.103, M.106, N.107, K.110, Q.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.110, A:Q.150 GOL.3: 5 residues within 4Å: Chain A: T.98, K.99, Q.142, E.146, R.149 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.98, A:K.99, A:E.146, A:R.149 Water bridges: A:T.98, A:T.98, A:S.145 GOL.4: 4 residues within 4Å: Chain A: D.196, G.198, E.201 Ligands: PO4.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.196, A:E.201 GOL.5: 3 residues within 4Å: Chain A: D.71, H.263, H.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.71, A:R.197 GOL.6: 8 residues within 4Å: Chain A: Y.48, Q.50, Q.51, D.70, D.71, H.92, R.197, E.201 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.51, A:R.197, A:E.201, A:E.201 Water bridges: A:D.70, A:D.71 GOL.7: 3 residues within 4Å: Chain A: D.97, K.99, A.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.99 GOL.8: 2 residues within 4Å: Chain A: R.31, R.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.31, A:R.34 GOL.9: 3 residues within 4Å: Chain A: R.81, T.83, G.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.81, A:G.84 Water bridges: A:G.84 GOL.10: 5 residues within 4Å: Chain A: R.11, Q.14, L.19, A.22, H.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.14

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

PO4.11: 5 residues within 4Å: Chain A: P.13, Q.14, S.15, Q.137, H.141 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.14, A:Q.137 Water bridges: A:H.141 Salt bridges: A:K.138, A:H.141 PO4.12: 3 residues within 4Å: Chain A: R.120, D.153, H.155 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.153 Salt bridges: A:H.155 PO4.13: 3 residues within 4Å: Chain A: E.6, P.25, R.120 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.6 Water bridges: A:L.4, A:E.6, A:R.120, A:H.155, A:H.155 Salt bridges: A:R.120 PO4.14: 8 residues within 4Å: Chain A: S.15, A.16, G.17, Q.137, T.140, V.161, T.162, E.163 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.16, A:G.17, A:T.162 Water bridges: A:Q.137, A:H.141 PO4.15: 6 residues within 4Å: Chain A: D.196, G.198, P.199, L.301, W.302 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.196, A:W.302, A:W.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J.S. et al., Structural Analyses on the Deamidation of N-Terminal Asn in the Human N-Degron Pathway. Biomolecules (2020)

Release Date

2019-12-11

Peptides

Protein N-terminal asparagine amidohydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein N-terminal asparagine amidohydrolase

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