SMTL ID : 7esr.1

Crystal structure of Synechocystis sp PCC6803 guanidinium hydrolase (R32)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-hexamer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.201, R.202, H.203, D.293, D.295 Ligands: CA.2, EDO.3 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 CA.2: 8 residues within 4Å: Chain A: H.176, H.199, D.201, H.203, D.205, D.293 Ligands: CA.1, EDO.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.176, A:D.201, A:D.205, A:D.293 CA.6: 7 residues within 4Å: Chain B: D.201, R.202, H.203, D.293, D.295 Ligands: CA.7, EDO.8 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 CA.7: 8 residues within 4Å: Chain B: H.176, H.199, D.201, H.203, D.205, D.293 Ligands: CA.6, EDO.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.176, B:D.201, B:D.205, B:D.293 CA.11: 7 residues within 4Å: Chain C: D.201, R.202, H.203, D.293, D.295 Ligands: CA.12, EDO.13 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 CA.12: 8 residues within 4Å: Chain C: H.176, H.199, D.201, H.203, D.205, D.293 Ligands: CA.11, EDO.13 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.176, C:D.201, C:D.205, C:D.293 CA.16: 7 residues within 4Å: Chain D: D.201, R.202, H.203, D.293, D.295 Ligands: CA.17, EDO.18 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.201, D:H.203, D:D.293, D:D.295, D:D.295 CA.17: 8 residues within 4Å: Chain D: H.176, H.199, D.201, H.203, D.205, D.293 Ligands: CA.16, EDO.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.176, D:D.201, D:D.205, D:D.293 CA.21: 7 residues within 4Å: Chain E: D.201, R.202, H.203, D.293, D.295 Ligands: CA.22, EDO.23 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.201, E:H.203, E:D.293, E:D.295, E:D.295 CA.22: 8 residues within 4Å: Chain E: H.176, H.199, D.201, H.203, D.205, D.293 Ligands: CA.21, EDO.23 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.176, E:D.201, E:D.205, E:D.293 CA.26: 7 residues within 4Å: Chain F: D.201, R.202, H.203, D.293, D.295 Ligands: CA.27, EDO.28 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.201, F:H.203, F:D.293, F:D.295, F:D.295 CA.27: 8 residues within 4Å: Chain F: H.176, H.199, D.201, H.203, D.205, D.293 Ligands: CA.26, EDO.28 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.176, F:D.201, F:D.205, F:D.293

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

EDO.3: 13 residues within 4Å: Chain A: H.176, H.199, D.201, H.203, D.205, H.216, T.217, D.293, D.295, W.307, E.338 Ligands: CA.1, CA.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.205, A:D.293 Water bridges: A:W.307, A:E.338 EDO.5: 9 residues within 4Å: Chain A: G.66, I.67, N.68, R.113 Chain F: N.68, Q.109, R.112, R.113 Ligands: EDO.30 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:N.68, A:N.68, F:Q.109 EDO.8: 13 residues within 4Å: Chain B: H.176, H.199, D.201, H.203, D.205, H.216, T.217, D.293, D.295, W.307, E.338 Ligands: CA.6, CA.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.205, B:D.293 Water bridges: B:W.307, B:E.338 EDO.10: 9 residues within 4Å: Chain B: G.66, I.67, N.68, R.113 Chain E: N.68, Q.109, R.112, R.113 Ligands: EDO.25 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:Q.109, B:N.68, B:N.68 EDO.13: 13 residues within 4Å: Chain C: H.176, H.199, D.201, H.203, D.205, H.216, T.217, D.293, D.295, W.307, E.338 Ligands: CA.11, CA.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.205, C:D.293 Water bridges: C:W.307, C:E.338 EDO.15: 9 residues within 4Å: Chain C: G.66, I.67, N.68, R.113 Chain D: N.68, Q.109, R.112, R.113 Ligands: EDO.20 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.68, C:N.68, D:Q.109 EDO.18: 13 residues within 4Å: Chain D: H.176, H.199, D.201, H.203, D.205, H.216, T.217, D.293, D.295, W.307, E.338 Ligands: CA.16, CA.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.205 Water bridges: D:W.307, D:E.338 EDO.20: 9 residues within 4Å: Chain C: N.68, Q.109, R.112, R.113 Chain D: G.66, I.67, N.68, R.113 Ligands: EDO.15 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.109, D:N.68, D:N.68 EDO.23: 13 residues within 4Å: Chain E: H.176, H.199, D.201, H.203, D.205, H.216, T.217, D.293, D.295, W.307, E.338 Ligands: CA.21, CA.22 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.205 Water bridges: E:W.307, E:E.338 EDO.25: 9 residues within 4Å: Chain B: N.68, Q.109, R.112, R.113 Chain E: G.66, I.67, N.68, R.113 Ligands: EDO.10 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:N.68, E:N.68, B:Q.109 EDO.28: 13 residues within 4Å: Chain F: H.176, H.199, D.201, H.203, D.205, H.216, T.217, D.293, D.295, W.307, E.338 Ligands: CA.26, CA.27 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.205 Water bridges: F:W.307, F:E.338 EDO.30: 9 residues within 4Å: Chain A: N.68, Q.109, R.112, R.113 Chain F: G.66, I.67, N.68, R.113 Ligands: EDO.5 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:N.68, F:N.68, A:Q.109

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

ACT.4: 4 residues within 4Å: Chain A: L.270, R.316, E.317, Y.320 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:R.316, A:R.316, A:E.317, B:T.266, B:T.266, B:T.266 Salt bridges: A:R.316 ACT.9: 4 residues within 4Å: Chain B: L.270, R.316, E.317, Y.320 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Water bridges: B:R.316, B:R.316, B:E.317, C:T.266, C:T.266, C:T.266 Salt bridges: B:R.316 ACT.14: 4 residues within 4Å: Chain C: L.270, R.316, E.317, Y.320 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Water bridges: C:R.316, C:R.316, C:E.317, A:T.266, A:T.266, A:T.266 Salt bridges: C:R.316 ACT.19: 4 residues within 4Å: Chain D: L.270, R.316, E.317, Y.320 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Water bridges: E:T.266, E:T.266, E:T.266, D:R.316, D:R.316 Salt bridges: D:R.316 ACT.24: 4 residues within 4Å: Chain E: L.270, R.316, E.317, Y.320 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain E Water bridges: F:T.266, F:T.266, F:T.266, E:R.316, E:R.316 Salt bridges: E:R.316 ACT.29: 4 residues within 4Å: Chain F: L.270, R.316, E.317, Y.320 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain F Water bridges: D:T.266, D:T.266, D:T.266, F:R.316, F:R.316 Salt bridges: F:R.316

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Probable agmatinase 2

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