SMTL ID : 3llx.1

Crystal structure of an ala racemase-like protein (il1761) from idiomarina loihiensis at 1.50 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: Y.177, H.347, C.349 Ligands: TRS.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.347, A:C.349, H2O.8 ZN.18: 4 residues within 4Å: Chain B: Y.177, H.347, C.349 Ligands: TRS.25 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.347, B:C.349, H2O.28

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: K.303, H.339 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: C.179, N.180, T.181, G.184 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: H.347 Chain B: W.280, R.285, S.318 Ligands: TRS.8 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: N.115, I.116, K.154 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: A.5, D.305, R.342, L.361 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.285, D.286, S.287 Chain B: R.285 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: K.303, H.339 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: C.179, N.180, T.181, G.184 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain A: W.280, R.285, S.318 Chain B: H.347 Ligands: TRS.25 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: N.115, I.116, K.154 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: A.5, D.305, R.342, L.361 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain A: R.285 Chain B: R.285, D.286, S.287 Ligand excluded by PLIP

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 11 residues within 4Å: Chain A: K.47, R.145, H.172, Y.177, H.347, C.349 Chain B: W.280, S.318, Q.319 Ligands: ZN.1, CL.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.145, A:Y.177, B:S.318 Water bridges: A:T.48, A:R.145 TRS.25: 11 residues within 4Å: Chain A: W.280, S.318, Q.319 Chain B: K.47, R.145, H.172, Y.177, H.347, C.349 Ligands: ZN.18, CL.21 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.318, A:Q.319, B:R.145, B:Y.177, B:Y.177 Water bridges: B:T.48, B:R.145

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

EDO.9: 6 residues within 4Å: Chain A: N.27, Y.30, F.241, V.250, C.251, H.255 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: D.295, G.297, N.315 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: W.273, N.315, S.316, V.323, E.325 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: V.89, G.90, L.112, E.138, R.145, G.146 Chain B: H.321 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: G.56, L.59, D.60, S.61, K.62, Y.82 Ligands: EDO.14 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: S.61, K.62 Ligands: EDO.13 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: D.194, R.197, I.198, N.201 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: Y.177, V.244, G.288, Q.292 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: E.53, T.369, W.370, Q.371 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: N.27, Y.30, F.241, V.250, C.251, H.255 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: D.295, G.297, N.315 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: W.273, N.315, S.316, V.323, E.325 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain A: H.321 Chain B: V.89, G.90, L.112, E.138, R.145, G.146 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain B: G.56, L.59, D.60, S.61, K.62, Y.82 Ligands: EDO.31 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: S.61, K.62 Ligands: EDO.30 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: D.194, R.197, I.198, N.201 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: Y.177, V.244, G.288, Q.292 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: E.53, T.369, W.370, Q.371 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of PROTEIN OF UNKNOWN FUNCTION (YP_156143.1) from Idiomarina loihiensis L2TR at 1.50 A resolution. To be published

Release Date

2010-02-09

Peptides

Predicted amino acid aldolase or racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Predicted amino acid aldolase or racemase