SMTL ID : 1nvm.1 (2 other biounits)

Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.18, H.200, H.202, N.236 Ligands: OXL.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.18, A:H.200, A:H.202, H2O.4 MN.8: 5 residues within 4Å: Chain C: D.18, H.200, H.202, N.236 Ligands: OXL.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.18, C:H.200, C:H.202, H2O.32

2 x OXL: OXALATE ION(Non-covalent)

OXL.2: 10 residues within 4Å: Chain A: R.17, D.18, L.88, F.139, M.141, S.171, H.200, H.202, Y.291 Ligands: MN.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.291, A:Y.291 Water bridges: A:R.17, A:R.17 Salt bridges: A:R.17, A:H.200, A:H.200, A:H.202 OXL.9: 11 residues within 4Å: Chain C: R.17, D.18, L.88, F.139, M.141, A.169, S.171, H.200, H.202, Y.291 Ligands: MN.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.291, C:Y.291 Water bridges: C:R.17, C:S.292 Salt bridges: C:R.17, C:H.200, C:H.200

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

SO4.3: 4 residues within 4Å: Chain A: T.28, L.29, R.66, H.67 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.29 Water bridges: A:T.28, A:T.28 Salt bridges: A:R.66, A:H.67 SO4.4: 2 residues within 4Å: Chain A: R.24, Q.26 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:N.259, A:Q.26 Salt bridges: A:R.24 SO4.10: 4 residues within 4Å: Chain C: T.28, L.29, R.66, H.67 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.29 Water bridges: C:T.28 Salt bridges: C:R.66, C:H.67 SO4.11: 2 residues within 4Å: Chain C: R.24, Q.26 7 PLIP interactions: 7 interactions with chain C Water bridges: C:R.24, C:R.24, C:R.24, C:R.24, C:Q.26, C:Q.26 Salt bridges: C:R.24 SO4.12: 4 residues within 4Å: Chain A: Y.287, V.314 Chain C: Y.258, M.261 No protein-ligand interaction detected (PLIP)

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 5 residues within 4Å: Chain A: A.174, S.176, D.179 Chain C: R.248, L.249 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.174 Hydrophobic interactions: C:L.249 Water bridges: C:R.248 MPD.7: 3 residues within 4Å: Chain B: E.61, L.90, Q.93 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.93 Hydrogen bonds: B:E.61, B:Q.93 MPD.13: 5 residues within 4Å: Chain A: R.248, L.249 Chain C: A.174, S.176, D.179 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:R.248, A:L.249 Water bridges: A:R.248, A:R.248 Hydrogen bonds: C:A.174 MPD.14: 2 residues within 4Å: Chain C: R.130, N.131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.131

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

NAD.6: 26 residues within 4Å: Chain B: I.10, G.11, S.12, G.13, N.14, I.15, V.36, G.37, I.38, G.59, A.78, T.79, S.80, L.103, T.104, P.105, C.132, S.163, G.165, P.166, G.167, T.168, N.171, N.290, L.291, M.294 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:I.15, B:M.294 Hydrogen bonds: B:S.12, B:S.12, B:N.14, B:N.14, B:I.15, B:S.42, B:T.79, B:A.81, B:G.165, B:G.167, B:T.168, B:T.168, B:N.171, B:N.171, B:N.290 Water bridges: B:S.12, B:G.13, B:N.14, B:G.16, B:I.38, B:V.60, B:V.60, B:N.87 NAD.15: 25 residues within 4Å: Chain D: I.10, G.11, S.12, G.13, N.14, I.15, G.37, I.38, A.78, T.79, S.80, A.83, L.103, T.104, P.105, C.132, S.163, G.165, P.166, G.167, T.168, N.171, N.290, L.291, M.294 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.15, D:M.294 Hydrogen bonds: D:S.12, D:S.12, D:N.14, D:N.14, D:I.15, D:T.79, D:A.81, D:G.165, D:G.167, D:T.168, D:T.168, D:N.171, D:N.171, D:N.290 Water bridges: D:G.13, D:N.14, D:G.16, D:I.38, D:S.42, D:A.83, D:N.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manjasetty, A.B. et al., Crystal structure of a bifunctional aldolase-dehydrogenase: Sequestering a reactive and volatile intermediate. Proc.Natl.Acad.Sci.USA (2003)

Release Date

2003-06-17

Peptides

4-hydroxy-2-oxovalerate aldolase: AC
acetaldehyde dehydrogenase (acylating): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

4-hydroxy-2-oxovalerate aldolase

acetaldehyde dehydrogenase (acylating)

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