SMTL ID : 4zm9.1 (1 other biounit)

Crystal structure of circularly permuted human asparaginase-like protein 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

3 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: L.55, E.56, D.58, F.61, A.63, C.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.58, A:F.61, A:A.63 NA.8: 7 residues within 4Å: Chain A: T.175, T.191, D.206, S.207, T.225, T.226 Ligands: GLY.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:T.225, G.2 NA.9: 6 residues within 4Å: Chain B: L.55, E.56, D.58, F.61, A.63, C.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.61, B:A.63, B:A.63

2 x GLY: GLYCINE(Non-covalent)

GLY.2: 13 residues within 4Å: Chain A: T.175, T.193, G.195, I.196, R.203, G.205, D.206, S.207, G.227, G.229, I.232 Ligands: DTT.7, NA.8 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:T.175, A:G.227, A:G.227, A:G.227, A:G.229, G.2 Water bridges: A:S.207 Salt bridges: A:R.203 GLY.10: 12 residues within 4Å: Chain B: T.175, T.193, G.195, I.196, R.203, G.205, D.206, S.207, G.227, G.229, I.232 Ligands: FLC.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.227, B:G.227, B:G.229 Water bridges: B:S.207, B:S.207 Salt bridges: B:R.203

5 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.3: 5 residues within 4Å: Chain A: R.239, E.246 Chain B: L.240, F.243, H.244 No protein-ligand interaction detected (PLIP) BME.4: 7 residues within 4Å: Chain A: S.88, A.89, V.108, M.109, T.112, H.114 Chain B: K.234 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.89, B:K.234 BME.5: 3 residues within 4Å: Chain A: A.54, D.57 Ligands: BME.6 No protein-ligand interaction detected (PLIP) BME.6: 5 residues within 4Å: Chain A: G.26, R.29, A.54, D.58 Ligands: BME.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.29, A:D.58, A:D.58 BME.12: 9 residues within 4Å: Chain A: K.234 Chain B: S.88, A.89, V.108, M.109, T.112, P.113, H.114, C.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.109

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.7: 10 residues within 4Å: Chain A: G.11, N.62, R.147, T.175, G.195, I.196, V.197, T.226, G.227 Ligands: GLY.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.147, A:R.147

1 x FLC: CITRATE ANION(Non-covalent)

FLC.11: 10 residues within 4Å: Chain B: G.10, G.11, N.62, R.147, T.175, G.195, I.196, T.226, G.227 Ligands: GLY.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.196 Hydrogen bonds: B:G.11, B:N.62, B:T.175, B:T.175, B:G.195, B:G.195, B:T.226, B:G.227 Salt bridges: B:R.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Intramolecular Cleavage of the hASRGL1 Homodimer Occurs in Two Stages. Biochemistry (2016)

Release Date

2016-02-17

Peptides

Isoaspartyl peptidase/L-asparaginase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoaspartyl peptidase/L-asparaginase

Related Entries With Identical Sequence