SMTL ID : 3lhl.2 (1 other biounit)

Crystal structure of a putative agmatinase from Clostridium difficile

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.98, D.121, D.125, D.202 Ligands: MN.2, MN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.98, A:D.121, A:D.125, A:D.202 MN.2: 6 residues within 4Å: Chain A: D.121, H.123, D.202, D.204 Ligands: MN.1, MN.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.121, A:H.123, A:D.202, A:D.204, A:D.204 MN.3: 6 residues within 4Å: Chain A: D.125, H.137, D.202, E.248 Ligands: MN.1, MN.2 No protein-ligand interaction detected (PLIP) MN.4: 5 residues within 4Å: Chain A: N.223 Chain B: N.223 Chain C: N.223 Ligands: MN.11, MN.18 No protein-ligand interaction detected (PLIP) MN.8: 6 residues within 4Å: Chain B: H.98, D.121, D.125, D.202 Ligands: MN.9, MN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.98, B:D.121, B:D.125, B:D.202 MN.9: 6 residues within 4Å: Chain B: D.121, H.123, D.202, D.204 Ligands: MN.8, MN.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.121, B:H.123, B:D.202, B:D.204, B:D.204 MN.10: 6 residues within 4Å: Chain B: D.125, H.137, D.202, E.248 Ligands: MN.8, MN.9 No protein-ligand interaction detected (PLIP) MN.11: 5 residues within 4Å: Chain A: N.223 Chain B: N.223 Chain C: N.223 Ligands: MN.4, MN.18 No protein-ligand interaction detected (PLIP) MN.15: 6 residues within 4Å: Chain C: H.98, D.121, D.125, D.202 Ligands: MN.16, MN.17 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.98, C:D.121, C:D.125, C:D.202 MN.16: 6 residues within 4Å: Chain C: D.121, H.123, D.202, D.204 Ligands: MN.15, MN.17 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.121, C:H.123, C:D.202, C:D.204, C:D.204 MN.17: 6 residues within 4Å: Chain C: D.125, H.137, D.202, E.248 Ligands: MN.15, MN.16 No protein-ligand interaction detected (PLIP) MN.18: 5 residues within 4Å: Chain A: N.223 Chain B: N.223 Chain C: N.223 Ligands: MN.4, MN.11 No protein-ligand interaction detected (PLIP)

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 7 residues within 4Å: Chain A: T.20, T.21, S.22, N.23, R.24, Y.130, H.137 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.22, A:N.23, A:R.24, A:Y.130, A:N.131 Salt bridges: A:H.137 PO4.6: 1 residues within 4Å: Chain A: R.86 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.86, A:R.86 Salt bridges: A:R.86 PO4.12: 7 residues within 4Å: Chain B: T.20, T.21, S.22, N.23, R.24, Y.130, H.137 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.22, B:N.23, B:R.24, B:Y.130, B:N.131 Salt bridges: B:H.137 PO4.13: 1 residues within 4Å: Chain B: R.86 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.86, B:R.86 Salt bridges: B:R.86 PO4.19: 7 residues within 4Å: Chain C: T.20, T.21, S.22, N.23, R.24, Y.130, H.137 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.22, C:N.23, C:R.24, C:Y.130, C:N.131 Salt bridges: C:H.137 PO4.20: 1 residues within 4Å: Chain C: R.86 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.86, C:R.86 Salt bridges: C:R.86

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 10 residues within 4Å: Chain A: V.12, F.13, G.14, S.31, M.34, R.35, F.38, D.59, G.61, L.267 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.12, A:F.38, A:L.267 Hydrogen bonds: A:R.35, A:R.35 MPD.14: 10 residues within 4Å: Chain B: V.12, F.13, G.14, S.31, M.34, R.35, F.38, D.59, G.61, L.267 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.12, B:F.38, B:L.267 Hydrogen bonds: B:R.35, B:R.35 MPD.21: 10 residues within 4Å: Chain C: V.12, F.13, G.14, S.31, M.34, R.35, F.38, D.59, G.61, L.267 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.12, C:F.38, C:L.267 Hydrogen bonds: C:R.35, C:R.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palani, K. et al., Crystal structure of a putative agmatinase from Clostridium difficile. To be Published

Release Date

2010-02-23

Peptides

Putative agmatinase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Putative agmatinase

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