SMTL ID : 2oqm.2 (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

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

EDO.1: 4 residues within 4Å: Chain A: H.171 Chain B: L.62, A.63, A.64 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.171 Water bridges: A:H.171, B:A.64 EDO.2: 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 B, 1 interactions with chain A Hydrogen bonds: B:I.151, A:L.24 EDO.9: 3 residues within 4Å: Chain B: H.171, N.172, G.173 No protein-ligand interaction detected (PLIP) EDO.10: 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: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.151, B:L.24 EDO.11: 4 residues within 4Å: Chain B: Q.90, Y.117, G.120, F.121 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.117, B:G.120 EDO.12: 4 residues within 4Å: Chain B: S.60, R.61, H.171, N.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.61, B:N.172 EDO.13: 3 residues within 4Å: Chain B: R.61, F.67 Ligands: CL.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.64

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

FMT.3: 3 residues within 4Å: Chain A: K.42, K.179, D.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.42 FMT.4: 5 residues within 4Å: Chain A: E.148, I.151, E.152 Chain B: D.23, V.27 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.152, B:D.23 FMT.5: 1 residues within 4Å: Chain A: V.26 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.27, A:S.30, A:K.34 FMT.6: 3 residues within 4Å: Chain A: Q.90, G.120, F.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.90, A:D.125 FMT.7: 5 residues within 4Å: Chain A: K.42, F.46, G.173, V.174, E.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.173, A:E.175 FMT.14: 4 residues within 4Å: Chain B: V.26, V.27, S.30, E.119 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Y.22, B:S.30, B:L.115, B:L.118 FMT.15: 1 residues within 4Å: Chain B: E.13 No protein-ligand interaction detected (PLIP) FMT.16: 5 residues within 4Å: Chain A: D.65 Chain B: R.170, G.173, V.174, E.175 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.173, B:E.175 FMT.17: 4 residues within 4Å: Chain B: A.130, T.145, Y.147, E.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.145, B:E.148

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

CL.8: 5 residues within 4Å: Chain B: R.61, F.67, N.68, R.71 Ligands: EDO.13 Ligand excluded by PLIP

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
C

B
D

Hypothetical protein

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