SMTL ID : 3no6.1

Crystal structure of a putative thiaminase II (SE1693) from Staphylococcus epidermidis ATCC 12228 at 1.65 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 7 residues within 4Å: Chain A: D.63, Y.66, Y.132, C.156, Y.160, E.227, F.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.63 Water bridges: A:Y.59 pi-Stacking: A:Y.66 IMD.4: 8 residues within 4Å: Chain B: D.63, Y.66, Y.132, C.156, Y.160, E.227, F.230 Ligands: MPD.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.227 pi-Stacking: B:Y.66 IMD.7: 6 residues within 4Å: Chain C: D.63, F.70, C.156, Y.160, E.227, F.230 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.63, C:E.227 pi-Stacking: C:F.230 IMD.14: 7 residues within 4Å: Chain D: D.63, F.70, C.156, Y.160, E.227, F.230 Ligands: MPD.18 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.63, D:D.63, D:Y.160 pi-Stacking: D:F.230

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

ACT.2: 4 residues within 4Å: Chain A: L.67, K.68, T.71, M.97 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.68 Salt bridges: A:K.68 ACT.3: 3 residues within 4Å: Chain A: F.138 Chain B: Y.137 Chain D: P.79 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:P.79, B:Y.137 ACT.12: 5 residues within 4Å: Chain B: P.79 Chain C: F.138, R.143 Chain D: N.72, Y.137 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Salt bridges: C:R.143 Hydrophobic interactions: D:Y.137 Water bridges: D:N.72 ACT.19: 3 residues within 4Å: Chain D: R.228, H.229 Ligands: MPD.16 4 PLIP interactions: 4 interactions with chain D Water bridges: D:R.228, D:R.228 Salt bridges: D:R.228, D:H.229 ACT.20: 3 residues within 4Å: Chain C: F.138 Chain D: E.69, K.134 No protein-ligand interaction detected (PLIP) ACT.21: 2 residues within 4Å: Chain D: S.52, N.53 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.53 Water bridges: D:Q.54

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

MPD.5: 8 residues within 4Å: Chain A: E.69, N.72, W.125, Y.137 Chain B: F.138, A.142, R.143 Chain C: P.79 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:W.125, A:Y.137, C:P.79 Hydrogen bonds: B:R.143, B:R.143 Water bridges: C:P.79 MPD.6: 9 residues within 4Å: Chain B: L.67, F.70, M.97, C.156, Y.160, Y.186, M.190, L.193 Ligands: IMD.4 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.67, B:F.70, B:Y.160, B:L.193 MPD.10: 10 residues within 4Å: Chain C: P.127, S.128, H.131 Chain D: P.127, S.128, H.131, H.229, E.238 Ligands: MPD.11, MPD.16 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:P.127, C:P.127 Hydrogen bonds: D:H.131, C:H.131 Water bridges: D:H.226, D:H.229, C:S.128, C:H.226, C:H.226 MPD.11: 8 residues within 4Å: Chain C: S.128, H.229, N.232, M.233, I.236, E.238 Ligands: MPD.10, MPD.16 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.236 Hydrogen bonds: C:H.229, C:N.232 Water bridges: C:H.229 MPD.16: 8 residues within 4Å: Chain D: S.128, H.229, N.232, M.233, E.238 Ligands: MPD.10, MPD.11, ACT.19 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.229, D:N.232 MPD.17: 7 residues within 4Å: Chain B: M.76, F.141 Chain D: M.76, P.79, K.80, A.140, F.141 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.141, D:F.141 MPD.18: 11 residues within 4Å: Chain D: L.67, F.70, Y.74, M.97, Y.132, M.153, C.156, P.157, L.193 Ligands: IMD.14, MRD.15 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.67, D:F.70 Hydrogen bonds: D:Y.74

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.8: 6 residues within 4Å: Chain A: M.76, F.141 Chain C: M.76, P.79, K.80, A.140 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:P.79, A:F.141 MRD.9: 5 residues within 4Å: Chain A: P.79, E.144 Chain C: Y.137 Chain D: F.138, R.143 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Water bridges: A:K.80, A:E.144, A:E.144 Hydrophobic interactions: C:Y.137 MRD.15: 9 residues within 4Å: Chain D: D.63, L.67, V.102, C.156, Y.160, Y.186, M.190, L.193 Ligands: MPD.18 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.67, D:Y.160, D:L.193 Hydrogen bonds: D:Y.186

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.13: 3 residues within 4Å: Chain C: Y.74, M.153, C.156 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a putative thiaminase II (SE1693) from Staphylococcus epidermidis ATCC 12228 at 1.65 A resolution. To be Published

Release Date

2010-07-28

Peptides

Transcriptional activator TenA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Transcriptional activator TenA