SMTL ID : 1sed.1

Crystal Structure of Protein of Unknown Function YhaL from Bacillus subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: E.54, E.57 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.54, A:E.54, A:E.57, A:E.57 ZN.11: 2 residues within 4Å: Chain B: E.54, E.57 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.54, B:E.54, B:E.57, B:E.57 ZN.20: 2 residues within 4Å: Chain C: E.54, E.57 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.54, C:E.54, C:E.57, C:E.57

3 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: G.79 Ligands: GOL.9, GOL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.79 NA.12: 3 residues within 4Å: Chain B: G.79 Ligands: GOL.18, GOL.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.79 NA.21: 3 residues within 4Å: Chain C: G.79 Ligands: GOL.28, GOL.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.79

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

MPD.3: 3 residues within 4Å: Chain A: M.49, R.50, D.53 Ligand excluded by PLIP MPD.4: 5 residues within 4Å: Chain A: D.71, A.75, F.114 Ligands: MPD.5, MPD.8 Ligand excluded by PLIP MPD.5: 6 residues within 4Å: Chain A: V.87, H.88, M.111, F.114, D.115 Ligands: MPD.4 Ligand excluded by PLIP MPD.6: 2 residues within 4Å: Chain A: E.58, L.76 Ligand excluded by PLIP MPD.7: 2 residues within 4Å: Chain A: K.72, L.76 Ligand excluded by PLIP MPD.8: 4 residues within 4Å: Chain A: D.71, K.72, A.75 Ligands: MPD.4 Ligand excluded by PLIP MPD.13: 3 residues within 4Å: Chain B: M.49, R.50, D.53 Ligand excluded by PLIP MPD.14: 4 residues within 4Å: Chain B: D.71, A.75, F.114 Ligands: MPD.15 Ligand excluded by PLIP MPD.15: 7 residues within 4Å: Chain B: A.78, V.87, H.88, M.111, F.114, D.115 Ligands: MPD.14 Ligand excluded by PLIP MPD.16: 7 residues within 4Å: Chain B: E.14, I.17, Q.18, I.36, D.37 Chain C: R.12, Y.16 Ligand excluded by PLIP MPD.17: 1 residues within 4Å: Chain B: K.72 Ligand excluded by PLIP MPD.22: 6 residues within 4Å: Chain A: R.12, Y.16 Chain C: E.14, Q.18, I.36, D.37 Ligand excluded by PLIP MPD.23: 4 residues within 4Å: Chain C: M.49, R.50, D.53, Y.100 Ligand excluded by PLIP MPD.24: 6 residues within 4Å: Chain C: A.78, H.88, M.111, F.114, D.115 Ligands: MPD.25 Ligand excluded by PLIP MPD.25: 4 residues within 4Å: Chain C: D.71, A.75, F.114 Ligands: MPD.24 Ligand excluded by PLIP MPD.26: 3 residues within 4Å: Chain C: E.58, L.76 Ligands: MPD.27 Ligand excluded by PLIP MPD.27: 3 residues within 4Å: Chain C: K.72, L.76 Ligands: MPD.26 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: A.78, G.79, L.81 Ligands: NA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.78 Water bridges: A:E.83, A:E.83 GOL.10: 3 residues within 4Å: Chain A: G.79, Q.80 Ligands: NA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.80 GOL.18: 5 residues within 4Å: Chain B: A.78, G.79, L.81 Ligands: NA.12, GOL.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.78 Water bridges: B:E.83, B:E.83 GOL.19: 4 residues within 4Å: Chain B: G.79, Q.80 Ligands: NA.12, GOL.18 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.79 GOL.28: 6 residues within 4Å: Chain C: A.78, G.79, Q.80, L.81, E.83 Ligands: NA.21 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.78 Water bridges: C:E.83, C:E.83 GOL.29: 3 residues within 4Å: Chain C: G.79, Q.80 Ligands: NA.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., The Crystal Structure of the Hypothetical Protein YhaI, APC1180 from Bacillus subtilis. To be Published

Release Date

2004-05-25

Peptides

Hypothetical protein yhaI: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hypothetical protein yhaI