SMTL ID : 6rgt.1

Crystal structure of the cofactor-free Aspergillus flavus urate oxidase T57A variant anaerobically complexed with 9-methyl uric acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x MUA: 9-METHYL URIC ACID(Non-covalent)

MUA.1: 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, A.58, D.59 10 PLIP interactions: 7 interactions with chain A, 3 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:A.58, B:D.59 pi-Stacking: A:F.160 Water bridges: B:V.56 MUA.5: 12 residues within 4Å: Chain A: Y.9, I.55, A.57, A.58, D.59 Chain B: F.160, L.171, R.177, S.227, V.228, Q.229, N.255 10 PLIP interactions: 7 interactions with chain B, 3 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:A.58, A:D.59 pi-Stacking: B:F.160 Water bridges: A:V.56 MUA.9: 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, A.58, D.59 10 PLIP interactions: 7 interactions with chain C, 3 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:A.58, D:D.59 pi-Stacking: C:F.160 Water bridges: D:V.56 MUA.13: 12 residues within 4Å: Chain C: Y.9, I.55, A.57, A.58, D.59 Chain D: F.160, L.171, R.177, S.227, V.228, Q.229, N.255 10 PLIP interactions: 7 interactions with chain D, 3 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:A.58, C:D.59 pi-Stacking: D:F.160 Water bridges: C:V.56

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

MPD.2: 4 residues within 4Å: Chain A: Q.159, W.161, W.175, N.224 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.161 Hydrogen bonds: A:Q.159 MPD.6: 4 residues within 4Å: Chain B: Q.159, W.161, W.175, N.224 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.161 Hydrogen bonds: B:Q.159 MPD.10: 4 residues within 4Å: Chain C: Q.159, W.161, W.175, N.224 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.161 Hydrogen bonds: C:Q.159 MPD.14: 4 residues within 4Å: Chain D: Q.159, W.161, W.175, N.224 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.161 Hydrogen bonds: D:Q.159

8 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 7 residues within 4Å: Chain A: V.4, K.5, A.6, A.7, G.41, I.43, E.44 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.5, A:G.41, A:I.43, A:E.44, A:E.44 Water bridges: A:A.7, A:A.7, A:G.41, A:G.41 TRS.4: 8 residues within 4Å: Chain A: D.12, N.13, T.34, V.35, C.36, N.101, I.102, V.103 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.12, A:N.13, A:C.36, A:N.101, A:V.103 Water bridges: A:D.12, A:D.12 TRS.7: 7 residues within 4Å: Chain B: V.4, K.5, A.6, A.7, G.41, I.43, E.44 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.5, B:G.41, B:I.43, B:E.44, B:E.44 Water bridges: B:A.7, B:A.7, B:G.41, B:G.41 TRS.8: 8 residues within 4Å: Chain B: D.12, N.13, T.34, V.35, C.36, N.101, I.102, V.103 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.12, B:N.13, B:C.36, B:N.101, B:V.103 Water bridges: B:D.12, B:D.12 TRS.11: 7 residues within 4Å: Chain C: V.4, K.5, A.6, A.7, G.41, I.43, E.44 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.5, C:G.41, C:I.43, C:E.44 Water bridges: C:A.7, C:A.7, C:E.40, C:E.40, C:E.40, C:G.41, C:G.41 TRS.12: 8 residues within 4Å: Chain C: D.12, N.13, T.34, V.35, C.36, N.101, I.102, V.103 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.12, C:N.13, C:C.36, C:N.101, C:V.103 Water bridges: C:D.12, C:D.12 TRS.15: 7 residues within 4Å: Chain D: V.4, K.5, A.6, A.7, G.41, I.43, E.44 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.5, D:G.41, D:I.43, D:E.44 Water bridges: D:A.7, D:A.7, D:E.40, D:E.40, D:E.40, D:G.41, D:G.41 TRS.16: 8 residues within 4Å: Chain D: D.12, N.13, T.34, V.35, C.36, N.101, I.102, V.103 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.12, D:N.13, D:C.36, D:N.101, D:V.103 Water bridges: D:D.12, D:D.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bui, S. et al., Crystal structure of the cofactor-free Aspergillus flavus urate oxidase T57A variant anaerobically complexed with 9-methyl uric acid. To Be Published

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