SMTL ID : 3ju7.1

Crystal structure of Putative PLP-dependent aminotransferase (NP_978343.1) from Bacillus cereus ATCC 10987 at 2.19 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 2 residues within 4Å: Chain A: D.20 Ligands: CA.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, H2O.6, H2O.6 CA.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: D.20 Ligands: CA.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, H2O.6, H2O.6 CA.11: 1 residues within 4Å: Chain B: D.20 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.20, H2O.11, H2O.12

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

ACT.4: 6 residues within 4Å: Chain A: N.33, F.218, N.232, K.234 Chain B: H.188, K.191 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.188, A:K.234 Hydrogen bonds: A:N.33 ACT.5: 4 residues within 4Å: Chain A: R.224 Chain B: R.316, L.317, Y.318 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.318 Water bridges: B:L.317 Salt bridges: B:R.316, A:R.224 Hydrogen bonds: A:R.224 ACT.6: 2 residues within 4Å: Chain A: K.153, G.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.153 ACT.12: 7 residues within 4Å: Chain A: H.188, K.191 Chain B: N.33, F.218, N.232, K.234 Ligands: PEG.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.33 Salt bridges: B:K.234, A:H.188 ACT.13: 4 residues within 4Å: Chain A: R.316, L.317, Y.318 Chain B: R.224 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.318 Water bridges: A:L.317 Salt bridges: A:R.316, B:R.224

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 3 residues within 4Å: Chain A: T.222, N.223, R.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.224, A:R.224 Water bridges: A:N.223 PEG.8: 9 residues within 4Å: Chain A: L.8, F.88, H.188, T.190, K.191, Q.289, Y.318 Chain B: N.33 Ligands: ACT.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.289 Water bridges: B:N.33 PEG.9: 7 residues within 4Å: Chain A: K.265, Q.281, T.283, E.284, A.285, V.286, Q.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.265, A:E.284, A:Q.288 Water bridges: A:V.286 PEG.14: 3 residues within 4Å: Chain B: T.222, N.223, R.224 No protein-ligand interaction detected (PLIP) PEG.15: 6 residues within 4Å: Chain B: L.8, T.190, K.191, Q.289, Y.318, F.319 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.190, B:Q.289 Water bridges: B:R.316 PEG.16: 4 residues within 4Å: Chain B: G.48, F.49, M.169, D.251 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.48 PEG.17: 5 residues within 4Å: Chain B: K.265, Q.281, T.283, E.284, Q.288 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.265, B:Q.288 Water bridges: B:V.286

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 10 residues within 4Å: Chain A: W.142, N.144, L.145, E.146, E.149, M.173, Y.175, G.176, Q.177, D.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.145, A:G.176 PGE.18: 11 residues within 4Å: Chain B: W.142, N.144, L.145, E.146, E.149, M.173, Y.175, G.176, Q.177, D.178, F.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.145, B:G.176, B:D.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative PLP-dependent aminotransferase (NP_978343.1) from Bacillus cereus ATCC 10987 at 2.19 A resolution. To be published

Release Date

2009-11-10

Peptides

Putative PLP-dependent aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative PLP-dependent aminotransferase