SMTL ID : 2pes.2 (1 other biounit)

Urate Oxidase in complex with tris-dipicolinate Lutetium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

12 x LU: LUTETIUM (III) ION(Non-functional Binders)

LU.1: 3 residues within 4Å: Ligands: PDC.5, PDC.6, PDC.7 No protein-ligand interaction detected (PLIP) LU.2: 3 residues within 4Å: Ligands: PDC.8, PDC.9, PDC.10 No protein-ligand interaction detected (PLIP) LU.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) LU.11: 3 residues within 4Å: Ligands: PDC.15, PDC.16, PDC.17 No protein-ligand interaction detected (PLIP) LU.12: 3 residues within 4Å: Ligands: PDC.18, PDC.19, PDC.20 No protein-ligand interaction detected (PLIP) LU.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) LU.21: 3 residues within 4Å: Ligands: PDC.25, PDC.26, PDC.27 No protein-ligand interaction detected (PLIP) LU.22: 3 residues within 4Å: Ligands: PDC.28, PDC.29, PDC.30 No protein-ligand interaction detected (PLIP) LU.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) LU.31: 3 residues within 4Å: Ligands: PDC.35, PDC.36, PDC.37 No protein-ligand interaction detected (PLIP) LU.32: 3 residues within 4Å: Ligands: PDC.38, PDC.39, PDC.40 No protein-ligand interaction detected (PLIP) LU.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

AZA.4: 12 residues within 4Å: Chain A: F.159, L.170, R.176, S.226, V.227, Q.228, N.254 Chain B: Y.8, I.54, A.56, T.57, D.58 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.176, A:R.176, A:V.227, A:Q.228, A:Q.228, A:N.254, B:T.57, B:D.58 pi-Stacking: A:F.159, A:F.159 Water bridges: B:T.57, B:T.57 AZA.14: 12 residues within 4Å: Chain A: Y.8, I.54, A.56, T.57, D.58 Chain B: F.159, L.170, R.176, S.226, V.227, Q.228, N.254 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:T.57, A:D.58, B:R.176, B:R.176, B:V.227, B:Q.228, B:Q.228, B:N.254 Water bridges: A:T.57, A:T.57 pi-Stacking: B:F.159, B:F.159 AZA.24: 12 residues within 4Å: Chain C: F.159, L.170, R.176, S.226, V.227, Q.228, N.254 Chain D: Y.8, I.54, A.56, T.57, D.58 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:T.57, D:D.58, C:R.176, C:R.176, C:V.227, C:Q.228, C:Q.228, C:N.254 pi-Stacking: C:F.159, C:F.159 AZA.34: 12 residues within 4Å: Chain C: Y.8, I.54, A.56, T.57, D.58 Chain D: F.159, L.170, R.176, S.226, V.227, Q.228, N.254 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.176, D:R.176, D:V.227, D:Q.228, D:Q.228, D:N.254, C:T.57, C:D.58 pi-Stacking: D:F.159, D:F.159

24 x PDC: PYRIDINE-2,6-DICARBOXYLIC ACID(Non-covalent)(Non-functional Binders)

PDC.5: 7 residues within 4Å: Chain A: P.202, K.203, A.206, Q.242 Ligands: LU.1, PDC.6, PDC.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.203, A:A.206 Hydrogen bonds: A:Q.242, A:Q.242 Salt bridges: A:K.203 PDC.6: 7 residues within 4Å: Chain A: S.199, H.200, P.202, K.203 Ligands: LU.1, PDC.5, PDC.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.199 Salt bridges: A:K.203 PDC.7: 4 residues within 4Å: Chain A: K.203 Ligands: LU.1, PDC.5, PDC.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.203 PDC.8: 4 residues within 4Å: Chain A: R.164 Ligands: LU.2, PDC.9, PDC.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.164 PDC.9: 7 residues within 4Å: Chain A: R.164, D.165, E.166, T.168 Ligands: LU.2, PDC.8, PDC.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.165 Salt bridges: A:R.164 PDC.10: 3 residues within 4Å: Ligands: LU.2, PDC.8, PDC.9 No protein-ligand interaction detected (PLIP) PDC.15: 7 residues within 4Å: Chain B: P.202, K.203, A.206, Q.242 Ligands: LU.11, PDC.16, PDC.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.203, B:A.206 Hydrogen bonds: B:Q.242, B:Q.242 Salt bridges: B:K.203 PDC.16: 7 residues within 4Å: Chain B: S.199, H.200, P.202, K.203 Ligands: LU.11, PDC.15, PDC.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.199 Salt bridges: B:K.203 PDC.17: 4 residues within 4Å: Chain B: K.203 Ligands: LU.11, PDC.15, PDC.16 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.203 PDC.18: 4 residues within 4Å: Chain B: R.164 Ligands: LU.12, PDC.19, PDC.20 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.164 PDC.19: 7 residues within 4Å: Chain B: R.164, D.165, E.166, T.168 Ligands: LU.12, PDC.18, PDC.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.165 Salt bridges: B:R.164 PDC.20: 3 residues within 4Å: Ligands: LU.12, PDC.18, PDC.19 No protein-ligand interaction detected (PLIP) PDC.25: 7 residues within 4Å: Chain C: P.202, K.203, A.206, Q.242 Ligands: LU.21, PDC.26, PDC.27 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.203, C:A.206 Hydrogen bonds: C:Q.242, C:Q.242 Salt bridges: C:K.203 PDC.26: 7 residues within 4Å: Chain C: S.199, H.200, P.202, K.203 Ligands: LU.21, PDC.25, PDC.27 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.199 Salt bridges: C:K.203 PDC.27: 4 residues within 4Å: Chain C: K.203 Ligands: LU.21, PDC.25, PDC.26 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.203 PDC.28: 4 residues within 4Å: Chain C: R.164 Ligands: LU.22, PDC.29, PDC.30 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.164 PDC.29: 7 residues within 4Å: Chain C: R.164, D.165, E.166, T.168 Ligands: LU.22, PDC.28, PDC.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.165 Salt bridges: C:R.164 PDC.30: 3 residues within 4Å: Ligands: LU.22, PDC.28, PDC.29 No protein-ligand interaction detected (PLIP) PDC.35: 7 residues within 4Å: Chain D: P.202, K.203, A.206, Q.242 Ligands: LU.31, PDC.36, PDC.37 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:K.203, D:A.206 Hydrogen bonds: D:Q.242, D:Q.242 Salt bridges: D:K.203 PDC.36: 7 residues within 4Å: Chain D: S.199, H.200, P.202, K.203 Ligands: LU.31, PDC.35, PDC.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.199 Salt bridges: D:K.203 PDC.37: 4 residues within 4Å: Chain D: K.203 Ligands: LU.31, PDC.35, PDC.36 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.203 PDC.38: 4 residues within 4Å: Chain D: R.164 Ligands: LU.32, PDC.39, PDC.40 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.164 PDC.39: 7 residues within 4Å: Chain D: R.164, D.165, E.166, T.168 Ligands: LU.32, PDC.38, PDC.40 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.165 Salt bridges: D:R.164 PDC.40: 3 residues within 4Å: Ligands: LU.32, PDC.38, PDC.39 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pompidor, G. et al., A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction. Acta Crystallogr.,Sect.D (2010)

Release Date

2008-04-22

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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