SMTL ID : 2oqm.1 (1 other biounit)

Crystal structure of a dinb family member protein (sden_0562) from shewanella denitrificans at 1.83 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: A.130, T.145, Y.147, E.148 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.145, A:T.145 EDO.2: 7 residues within 4Å: Chain A: Y.147, E.148, I.151, E.152 Chain B: D.23, V.27, Q.28 No protein-ligand interaction detected (PLIP) EDO.3: 8 residues within 4Å: Chain A: L.24, Q.28, F.29, I.155, Y.159 Chain B: I.151, I.155, P.156 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.159, B:I.151 EDO.4: 2 residues within 4Å: Chain A: D.41, R.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:D.41 EDO.14: 6 residues within 4Å: Chain A: F.17, Y.147 Chain B: G.19, M.20, D.23 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.19 EDO.15: 8 residues within 4Å: Chain A: I.151, I.155, P.156 Chain B: L.24, Q.28, F.29, I.155, Y.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.24, B:Y.159 EDO.16: 4 residues within 4Å: Chain A: H.171 Chain B: L.62, A.63, A.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.171 EDO.17: 3 residues within 4Å: Chain B: H.171, N.172, G.173 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.172 EDO.18: 4 residues within 4Å: Chain B: V.56, N.59, S.60 Ligands: EDO.19 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.55 EDO.19: 5 residues within 4Å: Chain B: S.60, R.61, H.171, N.172 Ligands: EDO.18 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.61, B:N.172 Water bridges: B:R.61, B:H.171, B:H.171

15 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 3 residues within 4Å: Chain A: N.59, S.60, R.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.61 FMT.6: 5 residues within 4Å: Chain A: Q.90, G.120, F.121, D.125 Ligands: FMT.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.90 FMT.7: 3 residues within 4Å: Chain A: V.26, S.30, E.119 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.30, A:E.119 FMT.8: 2 residues within 4Å: Chain A: D.23 Chain B: Y.147 No protein-ligand interaction detected (PLIP) FMT.9: 3 residues within 4Å: Chain A: D.55, V.56, N.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.55, A:N.59 FMT.10: 5 residues within 4Å: Chain A: Q.90, T.93, A.94, Y.117 Ligands: FMT.6 No protein-ligand interaction detected (PLIP) FMT.11: 2 residues within 4Å: Chain A: D.78, V.82 No protein-ligand interaction detected (PLIP) FMT.12: 5 residues within 4Å: Chain A: K.31, K.34, N.35, G.183, A.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.31, A:A.184 FMT.13: 5 residues within 4Å: Chain A: N.14, F.17, A.127, A.130, T.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.127 Water bridges: A:A.130 FMT.20: 5 residues within 4Å: Chain A: Q.66, F.160 Chain B: Y.166, R.170 Ligands: FMT.25 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.170 Water bridges: B:K.178, A:D.65 FMT.21: 3 residues within 4Å: Chain B: Y.22, V.26, E.119 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.30, B:K.34 FMT.22: 4 residues within 4Å: Chain B: K.42, F.46, V.174, E.175 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.175 FMT.23: 5 residues within 4Å: Chain B: K.31, K.34, N.35, G.183, A.184 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.31, B:A.184 FMT.24: 1 residues within 4Å: Chain B: T.103 No protein-ligand interaction detected (PLIP) FMT.25: 5 residues within 4Å: Chain A: F.67, F.160, H.161 Chain B: K.178 Ligands: FMT.20 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:H.161, A:H.161 Hydrogen bonds: B:K.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of hypothetical protein (YP_561575.1) from Shewanella denitrificans OS-217 at 1.83 A resolution. To be published

Release Date

2007-02-13

Peptides

Hypothetical protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hypothetical protein

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