SMTL ID : 4dz4.1

X-ray crystal structure of a hypothetical Agmatinase from Burkholderia thailandensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.163, H.165, D.246, D.248 Ligands: MN.2, UNK.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.163, A:H.165, A:D.246, A:D.248, H2O.10 MN.2: 7 residues within 4Å: Chain A: H.139, D.163, D.167, D.246 Ligands: MN.1, UNK.7, UNK.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.139, A:D.163, A:D.167, A:D.246, UNK.7 MN.10: 7 residues within 4Å: Chain B: H.139, D.163, D.167, D.246 Ligands: MN.11, UNK.22, UNK.23 6 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:H.139, B:D.163, B:D.167, B:D.246, H2O.21, UNK.22 MN.11: 6 residues within 4Å: Chain B: D.163, H.165, D.246, D.248 Ligands: MN.10, UNK.23 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.163, B:H.165, B:D.246, B:D.248, H2O.21 MN.24: 6 residues within 4Å: Chain C: D.163, H.165, D.246, D.248 Ligands: MN.25, UNK.34 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.163, C:H.165, C:D.246, C:D.248, H2O.32 MN.25: 7 residues within 4Å: Chain C: H.139, D.163, D.167, D.246 Ligands: MN.24, UNK.34, UNK.35 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.139, C:D.163, C:D.167, C:D.246, UNK.35 MN.36: 6 residues within 4Å: Chain D: D.163, H.165, D.246, D.248 Ligands: MN.37, UNK.46 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.163, D:H.165, D:D.246, D:D.248, H2O.45 MN.37: 7 residues within 4Å: Chain D: H.139, D.163, D.167, D.246 Ligands: MN.36, UNK.46, UNK.47 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.139, D:D.163, D:D.167, D:D.246, H2O.45 MN.49: 7 residues within 4Å: Chain E: H.139, D.163, D.167, D.246 Ligands: MN.50, UNK.60, UNK.61 6 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: E:H.139, E:D.163, E:D.167, E:D.246, H2O.56, UNK.61 MN.50: 6 residues within 4Å: Chain E: D.163, H.165, D.246, D.248 Ligands: MN.49, UNK.60 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.163, E:H.165, E:D.246, E:D.248, H2O.56 MN.62: 6 residues within 4Å: Chain F: D.163, H.165, D.246, D.248 Ligands: MN.63, UNK.73 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.163, F:H.165, F:D.246, F:D.248, H2O.68 MN.63: 7 residues within 4Å: Chain F: H.139, D.163, D.167, D.246 Ligands: MN.62, UNK.72, UNK.73 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.139, F:D.163, F:D.167, F:D.246, UNK.72

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

EDO.3: 8 residues within 4Å: Chain A: R.63, S.64, Y.295 Chain C: D.57, G.65, R.67, L.68, A.294 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: E.299 Chain B: L.68 Chain D: F.62, R.63, Y.295 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: L.68, S.71, A.72, P.293, E.299 Ligands: EDO.21 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: S.23, A.81, E.82, L.83, N.84, D.91 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: W.169, W.205, N.206, D.207 Chain E: L.83, N.84 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: E.82 Chain C: T.61, W.169, T.260 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: S.23, A.81, E.82, L.83, N.84, D.91 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain B: T.61, H.165, W.169, H.179, G.180, T.260 Chain E: E.82 Ligands: UNK.23 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: L.68 Chain B: A.75, E.299 Chain C: F.62, R.63, Y.295 Ligands: EDO.21 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain B: R.63, S.64, Y.295 Chain D: D.57, G.65, R.67, L.68, A.294 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: P.111, L.112, I.114, K.115, Y.140, D.175, L.177 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: S.24, E.26, N.27, T.28, V.78, A.81, E.82 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: I.15, R.16 Chain B: T.41, R.42, D.43 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: A.72, A.75, E.299 Ligands: EDO.5, EDO.16 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain C: S.23, A.81, E.82, L.83, N.84, D.91 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: L.83, N.84 Chain C: W.169, W.205, N.206, D.207 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain A: D.57, G.65, R.67, L.68, A.294 Chain C: R.63, S.64, Y.295 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain C: R.131, W.316, K.320 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: L.68, S.71, A.72, P.293 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain C: E.299 Chain E: F.62, R.63, Y.295 Chain F: L.68 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain C: P.111, L.112, I.114, K.115, Y.140, D.175, S.176, L.177 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: A.225, A.269, Q.270 Chain C: H.221 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain D: R.131, W.316, R.319, K.320 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain D: Y.21, G.22, D.94 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain D: S.23, A.81, E.82, L.83, N.84, D.91 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain D: E.82, L.83 Chain F: W.169, T.181 Ligand excluded by PLIP EDO.42: 8 residues within 4Å: Chain B: D.57, G.65, R.67, L.68, A.294 Chain D: R.63, S.64, Y.295 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain D: L.68, S.71, A.72, P.293, E.299 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain D: E.299 Chain E: L.68 Chain F: F.62, R.63, Y.295 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain A: L.83, N.84 Chain D: W.169, W.205, N.206, D.207 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain E: R.131, W.316, R.319, K.320 Ligand excluded by PLIP EDO.52: 6 residues within 4Å: Chain E: S.23, A.81, E.82, L.83, N.84, D.91 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain C: L.83, N.84 Chain E: W.169, W.205, N.206, D.207 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain B: W.205, Y.209, V.214 Chain E: Y.86 Ligand excluded by PLIP EDO.55: 9 residues within 4Å: Chain E: F.62, R.63, S.64, Y.295 Chain F: D.57, G.65, R.67, L.68, A.294 Ligand excluded by PLIP EDO.56: 4 residues within 4Å: Chain E: L.68, S.71, A.72, P.293 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain B: F.62, R.63, Y.295 Chain D: L.68 Chain E: A.75, E.299 Ligand excluded by PLIP EDO.58: 7 residues within 4Å: Chain C: E.82 Chain E: T.61, H.165, W.169, H.179, T.260 Ligands: UNK.60 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain B: H.221 Chain E: A.225, A.269, Q.270, A.273 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain D: L.83, N.84 Chain F: W.169, W.205, N.206, D.207 Ligand excluded by PLIP EDO.65: 3 residues within 4Å: Chain F: W.219, H.223, R.231 Ligand excluded by PLIP EDO.66: 3 residues within 4Å: Chain F: P.87, W.88, R.276 Ligand excluded by PLIP EDO.67: 3 residues within 4Å: Chain F: R.131, W.316, K.320 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain F: L.68, S.71, A.72, P.293 Ligand excluded by PLIP EDO.69: 8 residues within 4Å: Chain E: D.57, G.65, R.67, L.68, A.294 Chain F: R.63, S.64, Y.295 Ligand excluded by PLIP EDO.70: 5 residues within 4Å: Chain A: H.221 Chain F: A.225, A.269, Q.270, A.273 Ligand excluded by PLIP EDO.71: 6 residues within 4Å: Chain A: F.62, R.63, Y.295 Chain C: L.68 Chain F: A.75, E.299 Ligand excluded by PLIP

14 x UNK: UNKNOWN(Non-functional Binders)

UNK.7: 8 residues within 4Å: Chain A: H.139, D.167, H.179, D.246, E.290 Ligands: MN.2, UNK.8, UNK.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.290 UNK.8: 10 residues within 4Å: Chain A: H.165, H.179, D.246, D.248, T.260, E.290 Ligands: MN.1, MN.2, UNK.7, UNK.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.260, A:T.260 Water bridges: A:E.290 UNK.9: 6 residues within 4Å: Chain A: H.165, D.167, H.179, G.180 Ligands: UNK.7, UNK.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.179 UNK.22: 7 residues within 4Å: Chain B: H.139, D.167, H.179, D.246, E.290 Ligands: MN.10, UNK.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.290, B:E.290 UNK.23: 10 residues within 4Å: Chain B: H.165, H.179, D.246, D.248, T.260, E.290 Ligands: MN.10, MN.11, EDO.15, UNK.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.248 UNK.34: 9 residues within 4Å: Chain C: H.165, H.179, D.246, D.248, T.260, E.290 Ligands: MN.24, MN.25, UNK.35 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.260 UNK.35: 7 residues within 4Å: Chain C: H.139, D.167, H.179, D.246, E.290 Ligands: MN.25, UNK.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.179 UNK.46: 9 residues within 4Å: Chain D: H.165, H.179, D.246, D.248, T.260 Ligands: MN.36, MN.37, UNK.47, UNK.48 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.248 UNK.47: 8 residues within 4Å: Chain D: H.139, D.167, H.179, D.246, E.290 Ligands: MN.37, UNK.46, UNK.48 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.246, D:E.290, D:E.290 UNK.48: 6 residues within 4Å: Chain D: H.165, D.167, H.179, G.180 Ligands: UNK.46, UNK.47 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.167 Water bridges: D:H.165 UNK.60: 9 residues within 4Å: Chain E: H.165, H.179, D.246, D.248, T.260 Ligands: MN.49, MN.50, EDO.58, UNK.61 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.248 UNK.61: 7 residues within 4Å: Chain E: H.139, D.167, H.179, D.246, E.290 Ligands: MN.49, UNK.60 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.290 UNK.72: 7 residues within 4Å: Chain F: H.139, D.167, H.179, D.246, E.290 Ligands: MN.63, UNK.73 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.290, F:E.290 UNK.73: 9 residues within 4Å: Chain F: H.165, H.179, D.246, D.248, T.260, E.290 Ligands: MN.62, MN.63, UNK.72 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Combining functional and structural genomics to sample the essential Burkholderia structome. Plos One (2013)

Release Date

2012-03-28

Peptides

Agmatinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Agmatinase