SMTL ID : 6rgm.1

urate oxidase under 130 bar of krypton

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

MPD.1: 3 residues within 4Å: Chain A: H.20, T.29, Y.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.29 Water bridges: A:T.29 MPD.2: 1 residues within 4Å: Chain A: S.193 No protein-ligand interaction detected (PLIP) MPD.3: 7 residues within 4Å: Chain A: T.64, I.67, T.68, Q.71, N.72, H.87 Chain B: Y.168 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.67, A:Q.71 Hydrogen bonds: A:N.72, A:N.72, A:H.87 MPD.12: 3 residues within 4Å: Chain B: H.20, T.29, Y.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.29 Water bridges: B:T.29 MPD.13: 1 residues within 4Å: Chain B: S.193 No protein-ligand interaction detected (PLIP) MPD.14: 7 residues within 4Å: Chain A: Y.168 Chain B: T.64, I.67, T.68, Q.71, N.72, H.87 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.67, B:Q.71 Hydrogen bonds: B:N.72, B:N.72, B:H.87 MPD.23: 3 residues within 4Å: Chain C: H.20, T.29, Y.31 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.31 Water bridges: C:T.29 MPD.24: 1 residues within 4Å: Chain C: S.193 No protein-ligand interaction detected (PLIP) MPD.25: 7 residues within 4Å: Chain C: T.64, I.67, T.68, Q.71, N.72, H.87 Chain D: Y.168 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.67, C:Q.71 Hydrogen bonds: C:N.72, C:N.72 MPD.34: 3 residues within 4Å: Chain D: H.20, T.29, Y.31 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.31 Water bridges: D:T.29 MPD.35: 1 residues within 4Å: Chain D: S.193 No protein-ligand interaction detected (PLIP) MPD.36: 7 residues within 4Å: Chain C: Y.168 Chain D: T.64, I.67, T.68, Q.71, N.72, H.87 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.67, D:Q.71 Hydrogen bonds: D:N.72, D:N.72

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

ACT.4: 3 residues within 4Å: Chain A: D.182, P.254, N.286 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.254 Hydrogen bonds: A:N.286 Water bridges: B:N.13, B:N.13 ACT.5: 4 residues within 4Å: Chain D: R.15, E.32, H.105, R.123 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.15 Salt bridges: D:R.15, D:H.105 ACT.6: 3 residues within 4Å: Chain A: K.5, G.41, E.44 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.44 Hydrogen bonds: A:G.41 Water bridges: A:A.7, A:A.7, A:G.41, A:G.41 ACT.15: 3 residues within 4Å: Chain B: D.182, P.254, N.286 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:N.13, A:N.13 Hydrophobic interactions: B:P.254 Hydrogen bonds: B:N.286 ACT.16: 4 residues within 4Å: Chain C: R.15, E.32, H.105, R.123 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.15 Salt bridges: C:R.15, C:H.105 ACT.17: 3 residues within 4Å: Chain B: K.5, G.41, E.44 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.44 Hydrogen bonds: B:G.41 Water bridges: B:A.7, B:A.7, B:G.41, B:G.41 ACT.26: 3 residues within 4Å: Chain C: D.182, P.254, N.286 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.254 Hydrogen bonds: C:D.182, C:N.286 Water bridges: D:N.13, D:N.13 ACT.27: 4 residues within 4Å: Chain B: R.15, E.32, H.105, R.123 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.15 Salt bridges: B:R.15, B:H.105 ACT.28: 3 residues within 4Å: Chain C: K.5, G.41, E.44 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:E.44 Hydrogen bonds: C:G.41 Water bridges: C:A.7, C:E.40, C:G.41, C:G.41 ACT.37: 3 residues within 4Å: Chain D: D.182, P.254, N.286 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:P.254 Hydrogen bonds: D:D.182, D:N.286 Water bridges: C:N.13, C:N.13 ACT.38: 4 residues within 4Å: Chain A: R.15, E.32, H.105, R.123 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.15 Salt bridges: A:R.15, A:H.105 ACT.39: 3 residues within 4Å: Chain D: K.5, G.41, E.44 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:E.44 Hydrogen bonds: D:G.41 Water bridges: D:A.7, D:E.40, D:G.41, D:G.41

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

AZA.7: 12 residues within 4Å: Chain A: F.160, L.171, R.177, S.227, V.228, Q.229, N.255 Chain B: Y.9, I.55, A.57, T.58, D.59 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.177, A:R.177, A:V.228, A:Q.229, A:Q.229, A:N.255, B:T.58, B:D.59 Water bridges: A:H.257, B:T.58, B:T.58 pi-Stacking: A:F.160, A:F.160 AZA.18: 12 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 13 PLIP interactions: 9 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 Water bridges: B:H.257, A:T.58, A:T.58 pi-Stacking: B:F.160, B:F.160 AZA.29: 12 residues within 4Å: Chain C: F.160, L.171, R.177, S.227, V.228, Q.229, N.255 Chain D: Y.9, I.55, A.57, T.58, D.59 11 PLIP interactions: 9 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 Water bridges: C:H.257 pi-Stacking: C:F.160, C:F.160 AZA.40: 12 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 11 PLIP interactions: 9 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 Water bridges: D:H.257 pi-Stacking: D:F.160, D:F.160

12 x KR: KRYPTON(Non-covalent)

KR.8: 2 residues within 4Å: Chain A: T.231, L.253 No protein-ligand interaction detected (PLIP) KR.9: 6 residues within 4Å: Chain A: V.16, Y.17, K.18, Y.31, M.33, V.74 No protein-ligand interaction detected (PLIP) KR.10: 5 residues within 4Å: Chain A: T.208, T.211, I.239, R.242, Q.243 No protein-ligand interaction detected (PLIP) KR.19: 2 residues within 4Å: Chain B: T.231, L.253 No protein-ligand interaction detected (PLIP) KR.20: 6 residues within 4Å: Chain B: V.16, Y.17, K.18, Y.31, M.33, V.74 No protein-ligand interaction detected (PLIP) KR.21: 5 residues within 4Å: Chain B: T.208, T.211, I.239, R.242, Q.243 No protein-ligand interaction detected (PLIP) KR.30: 2 residues within 4Å: Chain C: T.231, L.253 No protein-ligand interaction detected (PLIP) KR.31: 6 residues within 4Å: Chain C: V.16, Y.17, K.18, Y.31, M.33, V.74 No protein-ligand interaction detected (PLIP) KR.32: 5 residues within 4Å: Chain C: T.208, T.211, I.239, R.242, Q.243 No protein-ligand interaction detected (PLIP) KR.41: 2 residues within 4Å: Chain D: T.231, L.253 No protein-ligand interaction detected (PLIP) KR.42: 6 residues within 4Å: Chain D: V.16, Y.17, K.18, Y.31, M.33, V.74 No protein-ligand interaction detected (PLIP) KR.43: 5 residues within 4Å: Chain D: T.208, T.211, I.239, R.242, Q.243 No protein-ligand interaction detected (PLIP)

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

NA.11: 5 residues within 4Å: Chain A: I.89, Y.92, N.93, I.95, E.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.93, A:I.95 NA.22: 5 residues within 4Å: Chain B: I.89, Y.92, N.93, I.95, E.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.92, B:I.95 NA.33: 5 residues within 4Å: Chain C: I.89, Y.92, N.93, I.95, E.137 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.95, C:I.95, C:H.96 NA.44: 5 residues within 4Å: Chain D: I.89, Y.92, N.93, I.95, E.137 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.93, D:I.95, D:H.96

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

2020-05-13

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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