SMTL ID : 7lol.1

The structure of Agmatinase from E. Coli at 1.8 A displaying urea and agmatine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x AG2: AGMATINE(Non-covalent)

AG2.1: 6 residues within 4Å: Chain A: H.151, Y.155, H.163, T.244 Chain C: W.68 Ligands: URE.5 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.68 pi-Cation interactions: C:W.68 Hydrogen bonds: A:T.244 Water bridges: A:D.153 AG2.7: 6 residues within 4Å: Chain A: W.68 Chain B: H.151, Y.155, H.163, T.244 Ligands: URE.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.244 Water bridges: B:D.153 Hydrophobic interactions: A:W.68 pi-Cation interactions: A:W.68 AG2.13: 6 residues within 4Å: Chain B: W.68 Chain C: H.151, Y.155, H.163, T.244 Ligands: URE.17 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.244 Water bridges: C:D.153 Hydrophobic interactions: B:W.68 pi-Cation interactions: B:W.68 AG2.19: 6 residues within 4Å: Chain D: H.151, Y.155, H.163, T.244 Chain F: W.68 Ligands: URE.23 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:T.244, D:T.244 Water bridges: D:D.153 Hydrophobic interactions: F:W.68 pi-Cation interactions: F:W.68 AG2.25: 6 residues within 4Å: Chain D: W.68 Chain E: H.151, Y.155, H.163, T.244 Ligands: URE.29 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:W.68 pi-Cation interactions: D:W.68 Hydrogen bonds: E:T.244, E:T.244 Water bridges: E:D.153 AG2.31: 6 residues within 4Å: Chain E: W.68 Chain F: H.151, Y.155, H.163, T.244 Ligands: URE.35 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:W.68 pi-Cation interactions: E:W.68 Hydrogen bonds: F:T.244, F:T.244 Water bridges: F:D.153

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

MN.2: 6 residues within 4Å: Chain A: H.126, D.149, D.153, D.230 Ligands: MN.3, URE.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.126, A:D.149, A:D.153, A:D.230, H2O.1 MN.3: 6 residues within 4Å: Chain A: D.149, H.151, D.230, D.232 Ligands: MN.2, URE.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.149, A:H.151, A:D.230, A:D.232, H2O.1 MN.4: 5 residues within 4Å: Chain A: Q.281 Chain B: Q.281 Chain C: Q.281 Ligands: MN.10, MN.16 No protein-ligand interaction detected (PLIP) MN.8: 6 residues within 4Å: Chain B: H.126, D.149, D.153, D.230 Ligands: MN.9, URE.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.126, B:D.149, B:D.153, B:D.230, H2O.6 MN.9: 6 residues within 4Å: Chain B: D.149, H.151, D.230, D.232 Ligands: MN.8, URE.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.149, B:H.151, B:D.230, B:D.232, H2O.6 MN.10: 5 residues within 4Å: Chain A: Q.281 Chain B: Q.281 Chain C: Q.281 Ligands: MN.4, MN.16 No protein-ligand interaction detected (PLIP) MN.14: 6 residues within 4Å: Chain C: H.126, D.149, D.153, D.230 Ligands: MN.15, URE.17 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.126, C:D.149, C:D.153, C:D.230, H2O.12 MN.15: 6 residues within 4Å: Chain C: D.149, H.151, D.230, D.232 Ligands: MN.14, URE.17 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.149, C:H.151, C:D.230, C:D.232, H2O.12 MN.16: 5 residues within 4Å: Chain A: Q.281 Chain B: Q.281 Chain C: Q.281 Ligands: MN.4, MN.10 No protein-ligand interaction detected (PLIP) MN.20: 6 residues within 4Å: Chain D: H.126, D.149, D.153, D.230 Ligands: MN.21, URE.23 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.126, D:D.149, D:D.153, D:D.230, H2O.18 MN.21: 6 residues within 4Å: Chain D: D.149, H.151, D.230, D.232 Ligands: MN.20, URE.23 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.149, D:H.151, D:D.230, D:D.232, H2O.18 MN.22: 5 residues within 4Å: Chain D: Q.281 Chain E: Q.281 Chain F: Q.281 Ligands: MN.28, MN.34 No protein-ligand interaction detected (PLIP) MN.26: 6 residues within 4Å: Chain E: H.126, D.149, D.153, D.230 Ligands: MN.27, URE.29 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.126, E:D.149, E:D.153, E:D.230, H2O.23 MN.27: 6 residues within 4Å: Chain E: D.149, H.151, D.230, D.232 Ligands: MN.26, URE.29 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.149, E:H.151, E:D.230, E:D.232, H2O.23 MN.28: 5 residues within 4Å: Chain D: Q.281 Chain E: Q.281 Chain F: Q.281 Ligands: MN.22, MN.34 No protein-ligand interaction detected (PLIP) MN.32: 6 residues within 4Å: Chain F: H.126, D.149, D.153, D.230 Ligands: MN.33, URE.35 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.126, F:D.149, F:D.153, F:D.230, H2O.29 MN.33: 6 residues within 4Å: Chain F: D.149, H.151, D.230, D.232 Ligands: MN.32, URE.35 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.149, F:H.151, F:D.230, F:D.232, H2O.29 MN.34: 5 residues within 4Å: Chain D: Q.281 Chain E: Q.281 Chain F: Q.281 Ligands: MN.22, MN.28 No protein-ligand interaction detected (PLIP)

6 x URE: UREA(Non-functional Binders)

URE.5: 10 residues within 4Å: Chain A: H.126, H.151, D.153, H.163, D.230, D.232, E.274 Ligands: AG2.1, MN.2, MN.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.153, A:D.232, A:E.274 Water bridges: A:G.164, A:T.244 URE.11: 10 residues within 4Å: Chain B: H.126, H.151, D.153, H.163, D.230, D.232, E.274 Ligands: AG2.7, MN.8, MN.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.153, B:D.232, B:E.274 Water bridges: B:G.164, B:T.244 URE.17: 10 residues within 4Å: Chain C: H.126, H.151, D.153, H.163, D.230, D.232, E.274 Ligands: AG2.13, MN.14, MN.15 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.126, C:D.153, C:D.232, C:E.274 Water bridges: C:G.164, C:T.244 URE.23: 10 residues within 4Å: Chain D: H.126, H.151, D.153, H.163, D.230, D.232, E.274 Ligands: AG2.19, MN.20, MN.21 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.153, D:D.232 Water bridges: D:G.164 URE.29: 10 residues within 4Å: Chain E: H.126, H.151, D.153, H.163, D.230, D.232, E.274 Ligands: AG2.25, MN.26, MN.27 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.153, E:D.232 Water bridges: E:G.164 URE.35: 10 residues within 4Å: Chain F: H.126, H.151, D.153, H.163, D.230, D.232, E.274 Ligands: AG2.31, MN.32, MN.33 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.153, F:D.232 Water bridges: F:G.164

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

TRS.6: 14 residues within 4Å: Chain A: P.236, A.237, P.240, I.284 Chain B: P.236, A.237, P.240, I.284 Chain C: P.236, A.237, P.240, I.284 Ligands: TRS.12, TRS.18 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:P.236, A:A.237, B:P.236, C:P.236 TRS.12: 14 residues within 4Å: Chain A: P.236, A.237, P.240, I.284 Chain B: P.236, A.237, P.240, I.284 Chain C: P.236, A.237, P.240, I.284 Ligands: TRS.6, TRS.18 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:P.236, B:A.237, A:P.236, C:P.236 TRS.18: 14 residues within 4Å: Chain A: P.236, A.237, P.240, I.284 Chain B: P.236, A.237, P.240, I.284 Chain C: P.236, A.237, P.240, I.284 Ligands: TRS.6, TRS.12 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:P.236, C:A.237, A:P.236, B:P.236 TRS.24: 14 residues within 4Å: Chain D: P.236, A.237, P.240, I.284 Chain E: P.236, A.237, P.240, I.284 Chain F: P.236, A.237, P.240, I.284 Ligands: TRS.30, TRS.36 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: F:P.236, E:P.236, D:P.236, D:A.237 TRS.30: 14 residues within 4Å: Chain D: P.236, A.237, P.240, I.284 Chain E: P.236, A.237, P.240, I.284 Chain F: P.236, A.237, P.240, I.284 Ligands: TRS.24, TRS.36 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: F:P.236, E:P.236, E:A.237, D:P.236 TRS.36: 14 residues within 4Å: Chain D: P.236, A.237, P.240, I.284 Chain E: P.236, A.237, P.240, I.284 Chain F: P.236, A.237, P.240, I.284 Ligands: TRS.24, TRS.30 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: F:P.236, F:A.237, D:P.236, E:P.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maturana, P. et al., Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity. Int J Mol Sci (2021)

Release Date

2021-05-12

Peptides

Agmatinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Agmatinase

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