SMTL ID : 6ia3.1

urate oxidase under 220 bar (22 MPa) of argon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: I.89, Y.92, N.93, I.95, E.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.95, A:H.96, A:E.137 NA.8: 5 residues within 4Å: Chain B: I.89, Y.92, N.93, I.95, E.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.89, B:I.95, B:H.96 NA.15: 5 residues within 4Å: Chain C: I.89, Y.92, N.93, I.95, E.137 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.95, C:H.96 NA.22: 5 residues within 4Å: Chain D: I.89, Y.92, N.93, I.95, E.137 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.93, D:I.95

4 x AZA: 8-AZAXANTHINE(Non-covalent)

AZA.2: 13 residues within 4Å: Chain A: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 Chain B: Y.9, I.55, A.57, T.58, D.59 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:T.58, B:D.59, A:R.177, A:R.177, A:V.228, A:Q.229, A:Q.229, A:N.255 Water bridges: B:T.58, B:T.58 pi-Stacking: A:F.160, A:F.160 AZA.9: 13 residues within 4Å: Chain A: Y.9, I.55, A.57, T.58, D.59 Chain B: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.177, B:R.177, B:V.228, B:Q.229, B:Q.229, B:N.255, A:T.58, A:D.59 pi-Stacking: B:F.160, B:F.160 Water bridges: A:T.58, A:T.58 AZA.16: 13 residues within 4Å: Chain C: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 Chain D: Y.9, I.55, A.57, T.58, D.59 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.177, C:R.177, C:V.228, C:Q.229, C:Q.229, C:N.255, D:T.58, D:D.59 pi-Stacking: C:F.160, C:F.160 AZA.23: 13 residues within 4Å: Chain C: Y.9, I.55, A.57, T.58, D.59 Chain D: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.177, D:R.177, D:V.228, D:Q.229, D:Q.229, D:N.255, C:T.58, C:D.59 pi-Stacking: D:F.160, D:F.160

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

PO4.3: 5 residues within 4Å: Chain A: H.87, K.91 Chain B: E.167, Y.168 Chain D: K.267 9 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 5 interactions with chain A Hydrogen bonds: B:E.167, B:Y.168 Water bridges: D:K.267, A:H.87, A:K.91, A:K.91, A:K.91 Salt bridges: D:K.267, A:K.91 PO4.10: 5 residues within 4Å: Chain A: E.167, Y.168 Chain B: H.87, K.91 Chain C: K.267 9 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Water bridges: B:H.87, B:K.91, B:K.91, B:K.91, C:K.267 Salt bridges: B:K.91, C:K.267 Hydrogen bonds: A:E.167, A:Y.168 PO4.17: 5 residues within 4Å: Chain B: K.267 Chain C: H.87, K.91 Chain D: E.167, Y.168 10 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:E.167, D:E.167 Water bridges: D:Y.168, D:Y.168, C:H.87, C:K.91, C:K.91, C:K.91 Salt bridges: C:K.91, B:K.267 PO4.24: 5 residues within 4Å: Chain A: K.267 Chain C: E.167, Y.168 Chain D: H.87, K.91 10 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A, 4 interactions with chain C Water bridges: D:H.87, D:K.91, D:K.91, D:K.91, C:Y.168, C:Y.168 Salt bridges: D:K.91, A:K.267 Hydrogen bonds: C:E.167, C:E.167

8 x AR: ARGON(Non-covalent)

AR.4: 2 residues within 4Å: Chain A: T.231, L.253 No protein-ligand interaction detected (PLIP) AR.5: 7 residues within 4Å: Chain A: V.16, Y.17, K.18, Y.31, E.32, M.33, V.74 No protein-ligand interaction detected (PLIP) AR.11: 2 residues within 4Å: Chain B: T.231, L.253 No protein-ligand interaction detected (PLIP) AR.12: 7 residues within 4Å: Chain B: V.16, Y.17, K.18, Y.31, E.32, M.33, V.74 No protein-ligand interaction detected (PLIP) AR.18: 2 residues within 4Å: Chain C: T.231, L.253 No protein-ligand interaction detected (PLIP) AR.19: 7 residues within 4Å: Chain C: V.16, Y.17, K.18, Y.31, E.32, M.33, V.74 No protein-ligand interaction detected (PLIP) AR.25: 2 residues within 4Å: Chain D: T.231, L.253 No protein-ligand interaction detected (PLIP) AR.26: 7 residues within 4Å: Chain D: V.16, Y.17, K.18, Y.31, E.32, M.33, V.74 No protein-ligand interaction detected (PLIP)

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 5 residues within 4Å: Chain A: D.12, N.13 Chain B: D.182, P.254, N.286 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.254 Hydrogen bonds: A:N.13, A:N.13 MPD.7: 1 residues within 4Å: Chain A: S.193 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.193 MPD.13: 5 residues within 4Å: Chain A: D.182, P.254, N.286 Chain B: D.12, N.13 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.254 Hydrogen bonds: B:N.13, B:N.13 MPD.14: 1 residues within 4Å: Chain B: S.193 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.193 MPD.20: 5 residues within 4Å: Chain C: D.12, N.13 Chain D: D.182, P.254, N.286 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:P.254 Hydrogen bonds: C:N.13, C:N.13 Water bridges: C:D.12 MPD.21: 1 residues within 4Å: Chain C: S.193 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.193 MPD.27: 5 residues within 4Å: Chain C: D.182, P.254, N.286 Chain D: D.12, N.13 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.13, D:N.13 Water bridges: D:D.12 Hydrophobic interactions: C:P.254 MPD.28: 1 residues within 4Å: Chain D: S.193 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prange, T. et al., Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization. Acta Cryst. D (2022)

Release Date

2019-12-18

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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