SMTL ID : 4gvx.1 (1 other biounit)

Crystal structure of a short chain dehydrogenase homolog (target EFI-505321) from burkholderia multivorans, with bound NADP and L-fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 29 residues within 4Å: Chain A: G.14, S.17, G.18, I.19, A.38, R.39, H.40, V.62, E.63, L.64, Q.65, N.90, A.91, G.92, Y.117, I.138, S.139, S.140, Y.153, K.157, P.183, A.184, E.185, V.186, T.188, P.189, L.190, Y.191 Ligands: FUL.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.183 Hydrogen bonds: A:I.19, A:R.39, A:E.63, A:L.64, A:Q.65, A:N.90, A:V.186, A:V.186, A:T.188, A:T.188, A:L.190 Water bridges: A:G.20, A:R.39, A:R.39, A:R.39, A:H.40, A:N.90, A:K.157 Salt bridges: A:R.39, A:H.40 pi-Cation interactions: A:R.39 NAP.7: 29 residues within 4Å: Chain B: G.14, S.17, G.18, I.19, A.38, R.39, H.40, V.62, E.63, L.64, Q.65, N.90, A.91, G.92, Y.117, I.138, S.139, S.140, Y.153, K.157, P.183, A.184, E.185, V.186, T.188, P.189, L.190, Y.191 Ligands: FUL.9 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:P.183 Hydrogen bonds: B:S.17, B:S.17, B:S.17, B:I.19, B:R.39, B:E.63, B:L.64, B:Q.65, B:N.90, B:V.186, B:V.186, B:T.188, B:L.190 Water bridges: B:G.20, B:R.39, B:R.39, B:R.39, B:R.39, B:H.40, B:N.90, B:K.157 Salt bridges: B:R.39, B:H.40 pi-Cation interactions: B:R.39 NAP.11: 29 residues within 4Å: Chain C: G.14, S.17, G.18, I.19, A.38, R.39, H.40, V.62, E.63, L.64, Q.65, N.90, A.91, G.92, Y.117, I.138, S.139, S.140, Y.153, K.157, P.183, A.184, E.185, V.186, T.188, P.189, L.190, Y.191 Ligands: FUL.13 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:P.183 Hydrogen bonds: C:I.19, C:R.39, C:E.63, C:L.64, C:Q.65, C:N.90, C:Y.117, C:Y.153, C:V.186, C:V.186, C:T.188, C:L.190 Water bridges: C:G.20, C:R.39, C:R.39, C:R.39, C:H.40, C:H.40, C:N.90, C:K.157 Salt bridges: C:R.39, C:H.40 pi-Cation interactions: C:R.39 NAP.17: 29 residues within 4Å: Chain D: G.14, S.17, G.18, I.19, A.38, R.39, H.40, V.62, E.63, L.64, Q.65, N.90, A.91, G.92, Y.117, I.138, S.139, S.140, Y.153, K.157, P.183, A.184, E.185, V.186, T.188, P.189, L.190, Y.191 Ligands: FUL.19 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:P.183 Hydrogen bonds: D:S.17, D:S.17, D:S.17, D:I.19, D:R.39, D:E.63, D:L.64, D:Q.65, D:N.90, D:Y.117, D:Y.153, D:V.186, D:V.186, D:L.190 Water bridges: D:G.20, D:R.39, D:R.39, D:R.39, D:R.39, D:H.40, D:H.40, D:N.90, D:K.157 Salt bridges: D:R.39, D:H.40 pi-Cation interactions: D:R.39

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

CL.2: 4 residues within 4Å: Chain A: G.98, L.99, N.149 Chain B: A.170 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: A.170 Chain B: G.98, L.99, N.149 Ligands: EDO.5 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: G.98, L.99, N.149 Chain D: A.170 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain C: A.170 Chain D: G.98, L.99, N.149 Ligands: EDO.15 Ligand excluded by PLIP

4 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.3: 11 residues within 4Å: Chain A: N.94, S.140, K.141, T.142, Q.147, Y.153, A.184, E.185, Y.191, W.194 Ligands: NAP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:N.94, A:W.194 Hydrogen bonds: A:N.94, A:S.140, A:S.140, A:S.140, A:K.141, A:K.141, A:Q.147, A:Y.153, A:Y.191 FUL.9: 11 residues within 4Å: Chain B: N.94, S.140, K.141, T.142, Q.147, Y.153, A.184, E.185, Y.191, W.194 Ligands: NAP.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.94, B:W.194 Hydrogen bonds: B:N.94, B:S.140, B:S.140, B:S.140, B:K.141, B:K.141, B:Q.147, B:Y.153, B:Y.191 FUL.13: 11 residues within 4Å: Chain C: N.94, S.140, K.141, T.142, Q.147, Y.153, A.184, E.185, Y.191, W.194 Ligands: NAP.11 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:N.94, C:W.194 Hydrogen bonds: C:N.94, C:S.140, C:S.140, C:S.140, C:K.141, C:K.141, C:Q.147 FUL.19: 11 residues within 4Å: Chain D: N.94, S.140, K.141, T.142, Q.147, Y.153, A.184, E.185, Y.191, W.194 Ligands: NAP.17 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:N.94, D:W.194 Hydrogen bonds: D:N.94, D:S.140, D:S.140, D:S.140, D:K.141, D:K.141, D:Q.147

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.5: 6 residues within 4Å: Chain A: K.129, A.170, L.171, H.174 Chain B: L.99 Ligands: CL.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.129, A:H.174 Water bridges: B:L.99, B:D.100 EDO.6: 5 residues within 4Å: Chain A: P.234, R.235, S.237 Chain C: E.223, D.226 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.226, C:D.226, A:R.235, A:S.237 Water bridges: C:R.26 EDO.10: 5 residues within 4Å: Chain B: P.234, R.235, S.237 Chain D: E.223, D.226 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.235, B:S.237, D:D.226, D:D.226 Water bridges: B:S.237 EDO.15: 6 residues within 4Å: Chain C: K.129, A.170, L.171, H.174 Chain D: L.99 Ligands: CL.18 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.129, C:H.174 Water bridges: D:L.99, D:D.100 EDO.16: 5 residues within 4Å: Chain A: E.223, D.226 Chain C: P.234, R.235, S.237 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.226, C:R.235, C:S.237 Water bridges: A:R.26 EDO.20: 5 residues within 4Å: Chain B: E.223, D.226 Chain D: P.234, R.235, S.237 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:D.226, D:R.235, D:S.237 Water bridges: D:S.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Crystal structure of a short chain dehydrogenase homolog (target EFI-505321) from burkholderia multivorans, with bound NADP and L-fucose. To be Published

Release Date

2012-10-03

Peptides

3-oxoacyl-[acyl-carrier protein] reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

3-oxoacyl-[acyl-carrier protein] reductase

Related Entries With Identical Sequence