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

STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: N.76, V.77, G.78, Y.100, R.234 Ligands: NAD.3, COI.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.76, A:V.77, A:G.78 Salt bridges: A:R.234 SO4.2: 6 residues within 4Å: Chain A: V.97, P.98, A.99, F.310, H.314, T.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.99 Water bridges: A:S.325, A:S.325 Salt bridges: A:H.314 SO4.5: 7 residues within 4Å: Chain B: N.76, V.77, G.78, Y.100, R.234 Ligands: NAD.7, COI.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.76, B:V.77, B:G.78 Salt bridges: B:R.234 SO4.6: 6 residues within 4Å: Chain B: V.97, P.98, A.99, F.310, H.314, T.326 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.99 Water bridges: B:S.325, B:S.325 Salt bridges: B:H.314 SO4.9: 7 residues within 4Å: Chain C: N.76, V.77, G.78, Y.100, R.234 Ligands: NAD.11, COI.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.76, C:V.77, C:G.78 Salt bridges: C:R.234 SO4.10: 6 residues within 4Å: Chain C: V.97, P.98, A.99, F.310, H.314, T.326 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.99 Water bridges: C:S.325, C:S.325 Salt bridges: C:H.314 SO4.13: 7 residues within 4Å: Chain D: N.76, V.77, G.78, Y.100, R.234 Ligands: NAD.15, COI.16 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.76, D:V.77, D:G.78, D:Y.100, D:Y.100 Salt bridges: D:R.234 SO4.14: 6 residues within 4Å: Chain D: V.97, P.98, A.99, F.310, H.314, T.326 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.99 Water bridges: D:S.325, D:S.325 Salt bridges: D:H.314 SO4.17: 7 residues within 4Å: Chain E: N.76, V.77, G.78, Y.100, R.234 Ligands: NAD.19, COI.20 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.76, E:V.77, E:G.78, E:Y.100 Salt bridges: E:R.234 SO4.18: 6 residues within 4Å: Chain E: V.97, P.98, A.99, F.310, H.314, T.326 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:A.99 Water bridges: E:S.325, E:S.325 Salt bridges: E:H.314 SO4.21: 7 residues within 4Å: Chain F: N.76, V.77, G.78, Y.100, R.234 Ligands: NAD.23, COI.24 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.76, F:V.77, F:G.78, F:Y.100 Salt bridges: F:R.234 SO4.22: 6 residues within 4Å: Chain F: V.97, P.98, A.99, F.310, H.314, T.326 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:A.99 Water bridges: F:S.325, F:S.325 Salt bridges: F:H.314

6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 27 residues within 4Å: Chain A: Y.100, I.105, G.152, G.154, H.155, I.156, G.157, Y.174, D.175, P.176, Y.177, H.204, V.205, P.206, G.207, N.211, I.214, T.232, A.233, R.234, D.258, T.259, H.295, A.297, Y.298 Ligands: SO4.1, COI.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.105 Hydrogen bonds: A:H.155, A:I.156, A:G.157, A:Y.177, A:V.205, A:G.207, A:N.211, A:N.211, A:R.234, A:D.258, A:D.258, A:A.297, A:Y.298 Water bridges: A:G.154, A:H.155, A:H.155, A:H.155 Salt bridges: A:H.155, A:H.155 NAD.7: 27 residues within 4Å: Chain B: Y.100, I.105, G.152, G.154, H.155, I.156, G.157, Y.174, D.175, P.176, Y.177, H.204, V.205, P.206, G.207, N.211, I.214, T.232, A.233, R.234, D.258, T.259, H.295, A.297, Y.298 Ligands: SO4.5, COI.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.105 Hydrogen bonds: B:H.155, B:I.156, B:G.157, B:Y.177, B:V.205, B:G.207, B:N.211, B:N.211, B:R.234, B:D.258, B:D.258, B:A.297, B:Y.298 Water bridges: B:G.154, B:H.155, B:H.155, B:H.155 Salt bridges: B:H.155, B:H.155 NAD.11: 27 residues within 4Å: Chain C: Y.100, I.105, G.152, G.154, H.155, I.156, G.157, Y.174, D.175, P.176, Y.177, H.204, V.205, P.206, G.207, N.211, I.214, T.232, A.233, R.234, D.258, T.259, H.295, A.297, Y.298 Ligands: SO4.9, COI.12 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.105 Hydrogen bonds: C:H.155, C:I.156, C:G.157, C:Y.177, C:V.205, C:G.207, C:N.211, C:N.211, C:R.234, C:D.258, C:D.258, C:A.297, C:Y.298 Water bridges: C:G.154, C:H.155, C:H.155, C:H.155 Salt bridges: C:H.155, C:H.155 NAD.15: 27 residues within 4Å: Chain D: Y.100, I.105, G.152, G.154, H.155, I.156, G.157, Y.174, D.175, P.176, Y.177, H.204, V.205, P.206, G.207, N.211, I.214, T.232, A.233, R.234, D.258, T.259, H.295, A.297, Y.298 Ligands: SO4.13, COI.16 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.105 Hydrogen bonds: D:H.155, D:I.156, D:G.157, D:Y.177, D:V.205, D:G.207, D:N.211, D:N.211, D:R.234, D:D.258, D:A.297, D:Y.298 Water bridges: D:T.153, D:G.154, D:H.155, D:H.155 Salt bridges: D:H.155, D:H.155 NAD.19: 27 residues within 4Å: Chain E: Y.100, I.105, G.152, G.154, H.155, I.156, G.157, Y.174, D.175, P.176, Y.177, H.204, V.205, P.206, G.207, N.211, I.214, T.232, A.233, R.234, D.258, T.259, H.295, A.297, Y.298 Ligands: SO4.17, COI.20 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:I.105 Hydrogen bonds: E:H.155, E:I.156, E:G.157, E:Y.177, E:V.205, E:G.207, E:N.211, E:N.211, E:R.234, E:D.258, E:A.297, E:Y.298 Water bridges: E:T.153, E:G.154, E:H.155, E:H.155 Salt bridges: E:H.155, E:H.155 NAD.23: 27 residues within 4Å: Chain F: Y.100, I.105, G.152, G.154, H.155, I.156, G.157, Y.174, D.175, P.176, Y.177, H.204, V.205, P.206, G.207, N.211, I.214, T.232, A.233, R.234, D.258, T.259, H.295, A.297, Y.298 Ligands: SO4.21, COI.24 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:I.105 Hydrogen bonds: F:H.155, F:I.156, F:G.157, F:Y.177, F:V.205, F:G.207, F:N.211, F:N.211, F:R.234, F:D.258, F:A.297, F:Y.298 Water bridges: F:T.153, F:G.154, F:H.155, F:H.155 Salt bridges: F:H.155, F:H.155

6 x COI: 2-OXO-4-METHYLPENTANOIC ACID(Non-covalent)

COI.4: 10 residues within 4Å: Chain A: R.9, N.76, V.77, Y.100, R.234, H.295, Y.298, M.307 Ligands: SO4.1, NAD.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.298 Hydrogen bonds: A:N.76, A:V.77, A:G.78, A:R.234, A:R.234 Salt bridges: A:R.234 COI.8: 10 residues within 4Å: Chain B: R.9, N.76, V.77, Y.100, R.234, H.295, Y.298, M.307 Ligands: SO4.5, NAD.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.298 Hydrogen bonds: B:N.76, B:V.77, B:G.78, B:R.234, B:R.234 Salt bridges: B:R.234 COI.12: 10 residues within 4Å: Chain C: R.9, N.76, V.77, Y.100, R.234, H.295, Y.298, M.307 Ligands: SO4.9, NAD.11 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.298 Hydrogen bonds: C:N.76, C:V.77, C:G.78, C:R.234, C:R.234 Salt bridges: C:R.234 COI.16: 10 residues within 4Å: Chain D: R.9, N.76, V.77, Y.100, R.234, H.295, Y.298, M.307 Ligands: SO4.13, NAD.15 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.298 Hydrogen bonds: D:N.76, D:V.77, D:G.78, D:Y.100, D:Y.100, D:R.234, D:R.234 Salt bridges: D:R.234 COI.20: 10 residues within 4Å: Chain E: R.9, N.76, V.77, Y.100, R.234, H.295, Y.298, M.307 Ligands: SO4.17, NAD.19 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:Y.298 Hydrogen bonds: E:N.76, E:V.77, E:G.78, E:Y.100, E:R.234, E:R.234 Salt bridges: E:R.234 COI.24: 10 residues within 4Å: Chain F: R.9, N.76, V.77, Y.100, R.234, H.295, Y.298, M.307 Ligands: SO4.21, NAD.23 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:Y.298 Hydrogen bonds: F:N.76, F:V.77, F:G.78, F:Y.100, F:R.234, F:R.234 Salt bridges: F:R.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dengler, U. et al., Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. J.Mol.Biol. (1997)

Release Date

1997-06-16

Peptides

D-2-HYDROXYISOCAPROATE DEHYDROGENASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

D-2-HYDROXYISOCAPROATE DEHYDROGENASE

Related Entries With Identical Sequence