SMTL ID : 5vg3.1

Structure of Oxalate Decarboxylase from Bacillus subtilis at pH 4.6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-hexamer

Ligands

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

ACT.1: 12 residues within 4Å: Chain A: M.84, R.92, H.95, H.97, E.101, L.153, F.155, F.160, E.162, T.165, Y.200 Ligands: MN.11 Ligand excluded by PLIP ACT.2: 9 residues within 4Å: Chain A: V.243, I.245, A.260, V.262, R.270, E.333, Y.340, D.342, P.377 Ligand excluded by PLIP ACT.3: 2 residues within 4Å: Chain A: P.223, Y.224 Ligand excluded by PLIP ACT.4: 4 residues within 4Å: Chain A: E.221, V.222, Y.224, P.225 Ligand excluded by PLIP ACT.5: 5 residues within 4Å: Chain A: E.117, P.135, S.136, L.138 Chain C: P.276 Ligand excluded by PLIP ACT.6: 5 residues within 4Å: Chain A: G.108, S.109, G.127, E.128, E.147 Ligand excluded by PLIP ACT.7: 7 residues within 4Å: Chain A: Q.143, N.204, Q.205, L.206, P.207 Chain C: T.355, F.356 Ligand excluded by PLIP ACT.8: 6 residues within 4Å: Chain A: Y.104, M.105, I.106, G.129, L.261, I.285 Ligand excluded by PLIP ACT.12: 12 residues within 4Å: Chain B: M.84, R.92, H.95, H.97, E.101, L.153, F.155, F.160, E.162, T.165, Y.200 Ligands: MN.19 Ligand excluded by PLIP ACT.13: 8 residues within 4Å: Chain B: V.243, I.245, A.260, V.262, R.270, E.333, Y.340, P.377 Ligand excluded by PLIP ACT.14: 6 residues within 4Å: Chain B: H.56, R.58, N.163 Chain D: H.42, G.43, R.301 Ligand excluded by PLIP ACT.15: 5 residues within 4Å: Chain B: Y.104, M.105, I.106, G.129, I.285 Ligand excluded by PLIP ACT.20: 13 residues within 4Å: Chain C: V.82, M.84, R.92, H.95, H.97, E.101, L.153, F.155, F.160, E.162, T.165, Y.200 Ligands: MN.25 Ligand excluded by PLIP ACT.21: 9 residues within 4Å: Chain C: V.243, I.245, A.260, V.262, R.270, E.333, Y.340, D.342, P.377 Ligand excluded by PLIP ACT.26: 12 residues within 4Å: Chain D: M.84, R.92, H.95, H.97, E.101, L.153, F.155, F.160, E.162, T.165, Y.200 Ligands: MN.36 Ligand excluded by PLIP ACT.27: 9 residues within 4Å: Chain D: V.243, I.245, A.260, V.262, R.270, E.333, Y.340, D.342, P.377 Ligand excluded by PLIP ACT.28: 2 residues within 4Å: Chain D: P.223, Y.224 Ligand excluded by PLIP ACT.29: 4 residues within 4Å: Chain D: E.221, V.222, Y.224, P.225 Ligand excluded by PLIP ACT.30: 5 residues within 4Å: Chain D: E.117, P.135, S.136, L.138 Chain F: P.276 Ligand excluded by PLIP ACT.31: 5 residues within 4Å: Chain D: G.108, S.109, G.127, E.128, E.147 Ligand excluded by PLIP ACT.32: 7 residues within 4Å: Chain D: Q.143, N.204, Q.205, L.206, P.207 Chain F: T.355, F.356 Ligand excluded by PLIP ACT.33: 6 residues within 4Å: Chain D: Y.104, M.105, I.106, G.129, L.261, I.285 Ligand excluded by PLIP ACT.37: 12 residues within 4Å: Chain E: M.84, R.92, H.95, H.97, E.101, L.153, F.155, F.160, E.162, T.165, Y.200 Ligands: MN.44 Ligand excluded by PLIP ACT.38: 8 residues within 4Å: Chain E: V.243, I.245, A.260, V.262, R.270, E.333, Y.340, P.377 Ligand excluded by PLIP ACT.39: 6 residues within 4Å: Chain A: H.42, G.43, R.301 Chain E: H.56, R.58, N.163 Ligand excluded by PLIP ACT.40: 5 residues within 4Å: Chain E: Y.104, M.105, I.106, G.129, I.285 Ligand excluded by PLIP ACT.45: 13 residues within 4Å: Chain F: V.82, M.84, R.92, H.95, H.97, E.101, L.153, F.155, F.160, E.162, T.165, Y.200 Ligands: MN.50 Ligand excluded by PLIP ACT.46: 9 residues within 4Å: Chain F: V.243, I.245, A.260, V.262, R.270, E.333, Y.340, D.342, P.377 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 1 residues within 4Å: Chain A: E.146 No protein-ligand interaction detected (PLIP) GOL.16: 9 residues within 4Å: Chain B: D.41, H.42, G.43, T.44, R.301 Chain D: H.56, R.58, E.162, N.163 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:R.58, D:E.162, D:N.163, B:G.43, B:R.301 Water bridges: D:N.57, D:L.59, B:D.41, B:H.42 GOL.17: 4 residues within 4Å: Chain B: S.248, T.249, D.338, H.339 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.339 GOL.34: 1 residues within 4Å: Chain D: E.146 No protein-ligand interaction detected (PLIP) GOL.41: 9 residues within 4Å: Chain A: H.56, R.58, E.162, N.163 Chain E: D.41, H.42, G.43, T.44, R.301 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain A Hydrogen bonds: E:G.43, E:R.301, A:R.58, A:E.162, A:E.162, A:N.163 Water bridges: E:D.41, A:N.57, A:L.59 GOL.42: 4 residues within 4Å: Chain E: S.248, T.249, D.338, H.339 No protein-ligand interaction detected (PLIP)

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

MN.10: 5 residues within 4Å: Chain A: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.273, A:H.275, A:E.280, A:H.319, H2O.3, H2O.3 MN.11: 5 residues within 4Å: Chain A: H.95, H.97, E.101, H.140 Ligands: ACT.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.95, A:H.97, A:E.101, A:H.140, H2O.1 MN.18: 5 residues within 4Å: Chain B: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.273, B:H.275, B:E.280, B:H.319, H2O.19, H2O.19 MN.19: 5 residues within 4Å: Chain B: H.95, H.97, E.101, H.140 Ligands: ACT.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.95, B:H.97, B:E.101, B:H.140, H2O.18 MN.24: 5 residues within 4Å: Chain C: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.273, C:H.275, C:E.280, C:H.319, H2O.34, H2O.34 MN.25: 5 residues within 4Å: Chain C: H.95, H.97, E.101, H.140 Ligands: ACT.20 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.95, C:H.97, C:E.101, C:H.140, H2O.32 MN.35: 5 residues within 4Å: Chain D: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.273, D:H.275, D:E.280, D:H.319, H2O.50, H2O.50 MN.36: 5 residues within 4Å: Chain D: H.95, H.97, E.101, H.140 Ligands: ACT.26 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.95, D:H.97, D:E.101, D:H.140, H2O.48 MN.43: 5 residues within 4Å: Chain E: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.273, E:H.275, E:E.280, E:H.319, H2O.66, H2O.66 MN.44: 5 residues within 4Å: Chain E: H.95, H.97, E.101, H.140 Ligands: ACT.37 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.95, E:H.97, E:E.101, E:H.140, H2O.65 MN.49: 5 residues within 4Å: Chain F: H.273, H.275, E.280, H.319, E.333 6 PLIP interactions: 4 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.273, F:H.275, F:E.280, F:H.319, H2O.81, H2O.81 MN.50: 5 residues within 4Å: Chain F: H.95, H.97, E.101, H.140 Ligands: ACT.45 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.95, F:H.97, F:E.101, F:H.140, H2O.79

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

MPD.22: 8 residues within 4Å: Chain C: Y.104, M.105, I.106, E.128, G.129, I.285, V.330 Chain F: P.22 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.104, C:E.128, C:I.285 MPD.23: 6 residues within 4Å: Chain C: K.87 Chain F: I.11, G.13, D.14, G.16, T.18 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: F:I.11, F:I.11 Hydrogen bonds: F:D.14, C:K.87 Water bridges: C:K.87 MPD.47: 8 residues within 4Å: Chain C: P.22 Chain F: Y.104, M.105, I.106, E.128, G.129, I.285, V.330 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:Y.104, F:E.128, F:I.285 MPD.48: 6 residues within 4Å: Chain C: I.11, G.13, D.14, G.16, T.18 Chain F: K.87 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:I.11, C:I.11 Hydrogen bonds: C:D.14, F:K.87 Water bridges: F:K.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Angerhofer, A. et al., Structure of Oxalate Decarboxylase from Bacillus subtilis at pH 4.6. To be Published

Release Date

2017-10-18

Peptides

Oxalate decarboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Oxalate decarboxylase