SMTL ID : 2r0x.1

Crystal structure of a putative flavin reductase (ycdh, hs_1225) from haemophilus somnus 129pt at 1.06 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 2 residues within 4Å: Chain A: N.53, H.129 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.53 Hydrogen bonds: A:N.53 Salt bridges: A:H.129 ACT.2: 5 residues within 4Å: Chain A: V.19, T.34, S.36, Y.150, Y.155 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.19, A:Y.150 Hydrogen bonds: A:S.81, A:Y.155, A:Y.155 Water bridges: A:S.36 ACT.3: 2 residues within 4Å: Chain A: K.9, R.153 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.9 Salt bridges: A:R.153 ACT.4: 5 residues within 4Å: Chain A: S.40, V.41, T.42, D.43 Chain B: H.129 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:D.43 Hydrogen bonds: A:S.40 Water bridges: B:H.129 Salt bridges: B:H.129 ACT.5: 7 residues within 4Å: Chain A: G.26, E.27, T.28, G.29, H.31, H.61, N.65 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.27, A:T.28, A:G.29, A:G.29 Salt bridges: A:H.31, A:H.61 ACT.12: 2 residues within 4Å: Chain B: N.53, H.129 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.53 Hydrogen bonds: B:N.53 Salt bridges: B:H.129 ACT.13: 5 residues within 4Å: Chain B: V.19, T.34, S.36, Y.150, Y.155 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.19, B:Y.150 Hydrogen bonds: B:S.81, B:Y.155 Water bridges: B:S.36 ACT.14: 2 residues within 4Å: Chain B: K.9, R.153 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.9 Salt bridges: B:R.153 ACT.15: 5 residues within 4Å: Chain A: H.129 Chain B: S.40, V.41, T.42, D.43 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:H.129 Salt bridges: A:H.129 Hydrophobic interactions: B:D.43 Hydrogen bonds: B:S.40 ACT.16: 7 residues within 4Å: Chain B: G.26, E.27, T.28, G.29, H.31, H.61, N.65 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.27, B:T.28, B:G.29, B:G.29 Salt bridges: B:H.31, B:H.61

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

SO4.6: 2 residues within 4Å: Chain A: H.156, S.157 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:S.157, A:S.157 Hydrogen bonds: A:S.157 Salt bridges: A:H.156 SO4.7: 7 residues within 4Å: Chain A: G.32, F.33, A.56, R.57, A.58, Q.90, R.93 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.32, A:A.58, A:Q.90 Water bridges: A:G.32, A:R.57, A:R.57, A:R.93, A:R.93, A:R.93 Salt bridges: A:R.57, A:R.93 SO4.8: 4 residues within 4Å: Chain A: H.31, R.57, H.61, Q.90 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.90 Water bridges: A:H.31, A:H.31, A:H.61 Salt bridges: A:H.31, A:R.57, A:H.61 SO4.17: 2 residues within 4Å: Chain B: H.156, S.157 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.157 Water bridges: B:S.157, A:S.157 Salt bridges: B:H.156 SO4.18: 7 residues within 4Å: Chain B: G.32, F.33, A.56, R.57, A.58, Q.90, R.93 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.32, B:A.58, B:Q.90 Water bridges: B:G.32, B:R.57, B:R.57, B:R.93, B:R.93, B:R.93 Salt bridges: B:R.57, B:R.93 SO4.19: 4 residues within 4Å: Chain B: H.31, R.57, H.61, Q.90 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.90 Water bridges: B:H.31, B:H.61, B:H.61 Salt bridges: B:H.31, B:R.57, B:H.61

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

EDO.9: 2 residues within 4Å: Chain A: H.125 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:I.123, A:H.125 EDO.10: 4 residues within 4Å: Chain A: V.63, R.66, I.123 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.66 EDO.11: 3 residues within 4Å: Chain A: K.135, V.137 Chain B: V.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.3, B:V.3 Water bridges: A:K.135 EDO.20: 2 residues within 4Å: Chain B: H.125 Ligands: EDO.21 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.123, B:H.125 EDO.21: 4 residues within 4Å: Chain B: V.63, R.66, I.123 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.66 EDO.22: 3 residues within 4Å: Chain A: V.3 Chain B: K.135, V.137 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:K.135 Hydrogen bonds: A:V.3, A:V.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative flavin reductase (YP_719437.1) from Haemophilus somnus 129PT at 1.06 A resolution. To be published

Release Date

2007-09-04

Peptides

Possible flavin reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Possible flavin reductase