SMTL ID : 2i51.1

CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-related, FMN binding protein (NPUN_F5749) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.40 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 19 residues within 4Å: Chain A: Y.26, R.41, T.42, L.43, V.44, I.58, T.59, S.63, A.64, K.65 Chain B: Y.80, Q.87, R.89, L.168, L.170, R.177 Ligands: EDO.7, EDO.8, EDO.19 25 PLIP interactions: 16 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Y.26, A:T.42, A:V.44, B:Q.87, B:L.168, B:L.170 Hydrogen bonds: A:T.42, A:T.42, A:V.44, A:I.58, A:A.64, A:K.65, A:K.65, B:Q.87, B:R.177 Water bridges: A:R.46, A:D.60, A:S.63, A:Q.68, B:R.89, B:R.89, B:R.89 Salt bridges: A:R.41, A:K.65, B:R.89 FMN.14: 19 residues within 4Å: Chain A: Y.80, Q.87, R.89, L.168, L.170, R.177 Chain B: Y.26, R.41, T.42, L.43, V.44, I.58, T.59, S.63, A.64, K.65 Ligands: EDO.15, EDO.16, EDO.20 27 PLIP interactions: 11 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: A:Y.80, A:Y.80, A:Q.87, A:L.168, A:L.170, B:Y.26, B:T.42, B:V.44 Hydrogen bonds: A:Q.87, A:R.177, B:T.42, B:T.42, B:V.44, B:I.58, B:A.64, B:K.65, B:K.65 Water bridges: A:R.89, A:R.89, A:R.89, B:R.46, B:D.60, B:S.63, B:Q.68 Salt bridges: A:R.89, B:R.41, B:K.65

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

EDO.2: 4 residues within 4Å: Chain A: R.17, N.83, T.84, R.171 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: A.112, Q.115, E.116 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: M.2, S.3, L.4, R.8, D.51, T.52, N.53 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: E.76, R.89, M.90, A.91, Q.164, V.165, D.166 Ligands: EDO.13 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: M.2, N.53, R.182, Q.186 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: I.58, Q.124, F.125 Ligands: FMN.1 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: Q.124 Chain B: Q.175 Ligands: FMN.1 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: D.101, S.102, H.103, Q.104, D.105 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: P.73, L.94, T.95, L.96, H.103 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: S.99, D.100, Q.104, Q.107 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: T.61, R.62, S.63, A.64, A.66, D.67 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: E.76, R.89, Q.164 Chain B: Q.33, A.39 Ligands: EDO.5 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: L.170, Q.175 Chain B: Q.124 Ligands: FMN.14, EDO.16 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: I.58, D.60, Q.124, F.125 Ligands: FMN.14, EDO.15 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: Q.33, A.39 Chain B: E.76, R.89, Q.164 Ligands: EDO.18 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain B: E.76, R.89, M.90, A.91, Q.164, V.165, D.166 Ligands: EDO.17 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: S.63, A.64, P.130, G.131 Chain B: R.177 Ligands: FMN.1 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: R.177 Chain B: S.63, A.64, P.130, G.131 Ligands: FMN.14 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain B: G.1, M.2, S.3, L.4, R.8, D.51, T.52, N.53 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: N.35, R.37 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 2 residues within 4Å: Chain B: I.111, Q.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.115 Water bridges: B:A.112, B:I.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Uncharacterized conserved protein of COG5135 (ZP_00109616.1) from Nostoc punctiforme PCC 73102 at 1.40 A resolution. To be published

Release Date

2006-09-05

Peptides

Uncharacterized conserved protein of COG5135: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uncharacterized conserved protein of COG5135