SMTL ID : 7oi1.1

Crystal structure of Synechocystis sp PCC6803 guanidinium hydrolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: R.113 Chain B: R.113 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain C: R.113 Ligand excluded by PLIP

6 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 6 residues within 4Å: Chain A: D.201, H.203, D.293, D.295 Ligands: NI.3, CAC.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.201, A:H.203, A:D.293, A:D.295, A:D.295 NI.3: 6 residues within 4Å: Chain A: H.176, D.201, D.205, D.293 Ligands: NI.2, CAC.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.176, A:D.201, A:D.205, A:D.293 NI.9: 6 residues within 4Å: Chain B: H.176, D.201, D.205, D.293 Ligands: NI.10, CAC.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.176, B:D.201, B:D.205, B:D.293 NI.10: 6 residues within 4Å: Chain B: D.201, H.203, D.293, D.295 Ligands: NI.9, CAC.11 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.201, B:H.203, B:D.293, B:D.295, B:D.295 NI.14: 6 residues within 4Å: Chain C: D.201, H.203, D.293, D.295 Ligands: NI.15, CAC.16 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.201, C:H.203, C:D.293, C:D.295, C:D.295 NI.15: 6 residues within 4Å: Chain C: H.176, D.201, D.205, D.293 Ligands: NI.14, CAC.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.176, C:D.201, C:D.205, C:D.293

3 x CAC: CACODYLATE ION(Non-covalent)

CAC.4: 12 residues within 4Å: Chain A: H.176, D.201, H.203, D.205, H.216, T.217, D.293, D.295, W.307, E.338 Ligands: NI.2, NI.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.216 CAC.11: 12 residues within 4Å: Chain B: H.176, D.201, H.203, D.205, H.216, T.217, D.293, D.295, W.307, E.338 Ligands: NI.9, NI.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.338 CAC.16: 12 residues within 4Å: Chain C: H.176, D.201, H.203, D.205, H.216, T.217, D.293, D.295, W.307, E.338 Ligands: NI.14, NI.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.203, C:D.295 Water bridges: C:H.216, C:D.295

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: E.33, M.71, P.120, L.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.33, A:R.130 EDO.6: 1 residues within 4Å: Chain A: L.270 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.316, A:R.316 EDO.7: 5 residues within 4Å: Chain A: R.327, T.329, N.330, S.367, Q.369 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain B: E.33, M.71, K.72, P.120, L.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.33 EDO.17: 4 residues within 4Å: Chain C: E.33, M.71, P.120, L.135 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.33

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 2 residues within 4Å: Chain A: T.266, E.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Funck, D. et al., Discovery of a Ni 2+ -dependent guanidine hydrolase in bacteria. Nature (2022)

Release Date

2021-12-15

Peptides

Probable agmatinase 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Probable agmatinase 2

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