SMTL ID : 5cbp.1

Crystal Structure of Conjoint Pyrococcus furiosus L-asparaginase at 37 degree C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

hetero-2-2-mer

Ligands

2 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 12 residues within 4Å: Chain A: G.10, T.11, D.51, S.52, T.53, G.82, T.83, D.84, S.109 Chain D: Y.74, V.76 Ligands: GOL.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.11, A:T.11, A:T.11, A:S.52, A:T.53, A:T.53, A:T.83, A:D.84, A:D.84, A:D.84 Water bridges: A:I.12 Salt bridges: A:K.154 FLC.11: 12 residues within 4Å: Chain B: Y.74, V.76 Chain C: G.10, T.11, D.51, S.52, T.53, G.82, T.83, D.84, S.109 Ligands: GOL.16 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:T.11, C:T.11, C:T.11, C:S.52, C:T.53, C:T.83, C:D.84, C:D.84, C:D.84, C:D.84 Water bridges: C:I.12, C:D.51 Salt bridges: C:K.154

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: F.44, L.45, N.70, K.73, Y.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.44, A:K.73 GOL.3: 6 residues within 4Å: Chain A: V.71, K.72, Y.74, D.75, P.101, I.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.72, A:Y.74, A:D.75 GOL.6: 11 residues within 4Å: Chain A: D.84, M.110, K.154, T.157 Chain D: Y.33, G.34, A.35, G.36, R.73, Y.74 Ligands: FLC.1 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:A.35, D:G.36, D:G.36, D:R.73, A:K.154, A:K.154, A:T.157 GOL.7: 5 residues within 4Å: Chain A: I.170, I.171, V.180, V.181, N.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.171, A:V.180 GOL.9: 6 residues within 4Å: Chain A: E.22, A.23, S.24, N.49, D.51 Chain D: Y.40 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Water bridges: A:D.51 Hydrogen bonds: D:Y.40, D:Y.40 GOL.10: 7 residues within 4Å: Chain B: V.69, D.70, L.71, T.72, P.87, G.89, R.118 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.71, B:T.72, B:G.89, B:R.118, B:R.118 GOL.12: 5 residues within 4Å: Chain C: F.44, L.45, N.70, K.73, Y.74 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.44, C:K.73, C:Y.74 GOL.13: 6 residues within 4Å: Chain C: V.71, K.72, Y.74, D.75, P.101, I.102 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.72, C:Y.74 GOL.16: 11 residues within 4Å: Chain B: Y.33, G.34, A.35, G.36, R.73, Y.74 Chain C: D.84, M.110, K.154, T.157 Ligands: FLC.11 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:T.83, C:K.154, C:K.154, C:T.157, B:A.35, B:G.36, B:G.36, B:R.73 Water bridges: C:T.53 GOL.17: 5 residues within 4Å: Chain C: I.170, I.171, V.180, V.181, N.182 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.171, C:V.180 GOL.19: 6 residues within 4Å: Chain B: Y.40 Chain C: E.22, A.23, S.24, N.49, D.51 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.40 Water bridges: C:D.51 GOL.20: 7 residues within 4Å: Chain D: V.69, D.70, L.71, T.72, P.87, G.89, R.118 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.70, D:L.71, D:T.72, D:G.89, D:R.118, D:R.118

6 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 8 residues within 4Å: Chain A: M.1, I.3, D.38, C.39, E.40, D.41, I.128, T.132 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.40, A:I.128 IPA.5: 2 residues within 4Å: Chain A: S.159, R.160 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.160, A:R.160 Hydrogen bonds: A:R.160 IPA.8: 2 residues within 4Å: Chain A: L.45, D.46 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.45 Hydrogen bonds: A:D.46, A:D.46 IPA.14: 8 residues within 4Å: Chain C: M.1, I.3, D.38, C.39, E.40, D.41, I.128, T.132 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.40, C:I.128 IPA.15: 2 residues within 4Å: Chain C: S.159, R.160 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.160, C:R.160 Hydrogen bonds: C:R.160 IPA.18: 2 residues within 4Å: Chain C: L.45, D.46 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.45 Hydrogen bonds: C:D.46, C:D.46, C:D.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, P. et al., Heat induces end to end repetitive association in P. furiosus L-asparaginase which enables its thermophilic property. Sci Rep (2020)

Release Date

2016-07-06

Peptides

L-asparaginase: AC
L-asparaginase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

L-asparaginase

L-asparaginase

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