SMTL ID : 4e2s.2 (1 other biounit)

Crystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in complex with its substrate, (S)-Ureidoglycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-octamer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: E.203, H.205, H.209, Q.243 Ligands: UGY.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.203, A:H.205, A:H.209 MN.3: 5 residues within 4Å: Chain B: E.203, H.205, H.209, Q.243 Ligands: UGY.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.203, B:H.205, B:H.209, UGY.4 MN.5: 5 residues within 4Å: Chain C: E.203, H.205, H.209, Q.243 Ligands: UGY.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.203, C:H.205, C:H.209 MN.7: 5 residues within 4Å: Chain D: E.203, H.205, H.209, Q.243 Ligands: UGY.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:E.203, D:H.205, D:H.209, UGY.8 MN.9: 5 residues within 4Å: Chain E: E.203, H.205, H.209, Q.243 Ligands: UGY.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:E.203, E:H.205, E:H.209, UGY.10 MN.11: 5 residues within 4Å: Chain F: E.203, H.205, H.209, Q.243 Ligands: UGY.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.203, F:H.205, F:H.209 MN.13: 5 residues within 4Å: Chain G: E.203, H.205, H.209, Q.243 Ligands: UGY.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Ligand interactions Metal complexes: G:E.203, G:H.205, G:H.209, UGY.14 MN.15: 5 residues within 4Å: Chain H: E.203, H.205, H.209, Q.243 Ligands: UGY.16 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.203, H:H.205, H:H.209

8 x UGY: (2S)-amino(carbamoylamino)ethanoic acid(Non-covalent)

UGY.2: 12 residues within 4Å: Chain A: M.191, L.199, E.203, H.205, H.209, Y.220, M.237, Q.243, Y.255, L.257, K.259 Ligands: MN.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.220, A:Y.220, A:Y.255 Water bridges: A:H.189 Salt bridges: A:H.205, A:H.209, A:K.259 UGY.4: 12 residues within 4Å: Chain B: M.191, L.199, E.203, H.205, H.209, Y.220, M.237, Q.243, Y.255, L.257, K.259 Ligands: MN.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.220, B:Y.220, B:Y.255 Water bridges: B:H.189 Salt bridges: B:H.205, B:H.209, B:K.259 UGY.6: 11 residues within 4Å: Chain C: H.189, M.191, E.203, H.205, H.209, Y.220, Q.243, Y.255, L.257, K.259 Ligands: MN.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.220, C:Y.220 Water bridges: C:E.203 Salt bridges: C:H.189, C:H.205, C:H.209, C:K.259 UGY.8: 12 residues within 4Å: Chain D: M.191, L.199, E.203, H.205, H.209, Y.220, M.237, Q.243, Y.255, L.257, K.259 Ligands: MN.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.220, D:Y.220, D:Y.255 Salt bridges: D:H.205, D:H.209, D:K.259 UGY.10: 11 residues within 4Å: Chain E: M.191, E.203, H.205, H.209, Y.220, M.237, Q.243, Y.255, L.257, K.259 Ligands: MN.9 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Y.220, E:Q.243 Salt bridges: E:H.189, E:H.205, E:H.209, E:K.259 UGY.12: 12 residues within 4Å: Chain F: M.191, L.199, E.203, H.205, H.209, Y.220, M.237, Q.243, Y.255, L.257, K.259 Ligands: MN.11 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:Y.220, F:Y.220, F:Q.243 Salt bridges: F:H.205, F:H.209, F:K.259 UGY.14: 11 residues within 4Å: Chain G: M.191, E.203, H.205, H.209, Y.220, M.237, Q.243, Y.255, L.257, K.259 Ligands: MN.13 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:Y.220, G:Q.243 Salt bridges: G:H.205, G:H.209, G:K.259 UGY.16: 12 residues within 4Å: Chain H: M.191, L.199, E.203, H.205, H.209, Y.220, M.237, Q.243, Y.255, L.257, K.259 Ligands: MN.15 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:E.203, H:H.209, H:Y.220, H:Y.220, H:Y.255 Salt bridges: H:H.189, H:H.205, H:H.209, H:K.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, I. et al., Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana. J.Biol.Chem. (2012)

Release Date

2012-04-18

Peptides

Ureidoglycine aminohydrolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
H

D
L

E
M

F
N

G
O

H
P

Ureidoglycine aminohydrolase

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