SMTL ID : 1nvm.3 (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-4-4-mer

Ligands

4 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.9: 5 residues within 4Å: Chain C: D.18, H.200, H.202, N.236 Ligands: OXL.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.18, C:H.200, C:H.202, H2O.33 MN.15: 5 residues within 4Å: Chain E: D.18, H.200, H.202, N.236 Ligands: OXL.16 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.18, E:H.200, E:H.202, H2O.54 MN.22: 5 residues within 4Å: Chain G: D.18, H.200, H.202, N.236 Ligands: OXL.23 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.18, G:H.200, G:H.202, H2O.83

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 11 residues within 4Å: Chain A: R.17, D.18, L.88, F.139, M.141, A.169, S.171, H.200, H.202, Y.291 Ligands: MN.1 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.17, A:R.17, A:Y.291, A:S.292 Salt bridges: A:R.17, A:H.200, A:H.200 OXL.10: 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.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.291 Water bridges: C:Y.291, C:Y.291 Salt bridges: C:R.17, C:H.200, C:H.200 OXL.16: 10 residues within 4Å: Chain E: R.17, D.18, L.88, F.139, M.141, S.171, H.200, H.202, Y.291 Ligands: MN.15 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:Y.291, E:Y.291 Water bridges: E:R.17, E:R.17 Salt bridges: E:R.17, E:H.200, E:H.200, E:H.202 OXL.23: 11 residues within 4Å: Chain G: R.17, D.18, L.88, F.139, M.141, A.169, S.171, H.200, H.202, Y.291 Ligands: MN.22 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:Y.291, G:Y.291 Water bridges: G:R.17, G:S.292 Salt bridges: G:R.17, G:H.200, G:H.200

12 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, A:D.30 Water bridges: A:T.28 Salt bridges: A:R.66, A:H.67 SO4.4: 4 residues within 4Å: Chain A: L.257, Y.258, M.261 Chain C: L.310 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.258 SO4.5: 2 residues within 4Å: Chain A: K.8, H.82 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.8 Salt bridges: A:H.82 SO4.7: 5 residues within 4Å: Chain B: G.13, N.14, I.15, S.80, P.166 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.14, B:I.15, B:S.80, B:S.80 Water bridges: B:G.13, B:G.13, B:S.80 SO4.8: 4 residues within 4Å: Chain B: S.82, A.83, H.84, V.85 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.83, B:H.84, B:V.85, B:Q.86 SO4.11: 4 residues within 4Å: Chain C: T.28, L.29, R.66, H.67 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.29 Water bridges: C:T.28, C:D.30 Salt bridges: C:R.66, C:H.67 SO4.12: 4 residues within 4Å: Chain A: Y.287, L.310 Chain C: L.257, Y.258 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Y.258 SO4.17: 4 residues within 4Å: Chain E: T.28, L.29, R.66, H.67 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.29 Water bridges: E:T.28, E:T.28 Salt bridges: E:R.66, E:H.67 SO4.18: 2 residues within 4Å: Chain E: R.24, Q.26 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Water bridges: F:N.259, E:Q.26 Salt bridges: E:R.24 SO4.24: 4 residues within 4Å: Chain G: T.28, L.29, R.66, H.67 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:L.29 Water bridges: G:T.28 Salt bridges: G:R.66, G:H.67 SO4.25: 2 residues within 4Å: Chain G: R.24, Q.26 7 PLIP interactions: 7 interactions with chain G Water bridges: G:R.24, G:R.24, G:R.24, G:R.24, G:Q.26, G:Q.26 Salt bridges: G:R.24 SO4.26: 4 residues within 4Å: Chain E: Y.287, V.314 Chain G: Y.258, M.261 No protein-ligand interaction detected (PLIP)

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

MPD.6: 5 residues within 4Å: Chain A: A.174, S.176, D.179 Chain C: R.248, L.249 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.249 Hydrogen bonds: C:R.248, A:A.174 MPD.13: 5 residues within 4Å: Chain A: R.248, L.249 Chain C: A.174, S.176, D.179 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:R.248, A:L.249 Water bridges: A:R.248 Hydrogen bonds: C:A.174 MPD.19: 5 residues within 4Å: Chain E: A.174, S.176, D.179 Chain G: R.248, L.249 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:L.249 Water bridges: G:R.248 Hydrogen bonds: E:A.174 MPD.21: 3 residues within 4Å: Chain F: E.61, L.90, Q.93 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:Q.93 Hydrogen bonds: F:E.61, F:Q.93 MPD.27: 5 residues within 4Å: Chain E: R.248, L.249 Chain G: A.174, S.176, D.179 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:R.248, E:L.249 Water bridges: E:R.248, E:R.248 Hydrogen bonds: G:A.174 MPD.28: 2 residues within 4Å: Chain G: R.130, N.131 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.131

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

NAD.14: 25 residues within 4Å: Chain D: I.10, G.11, S.12, G.13, N.14, I.15, I.38, A.78, T.79, S.80, A.83, L.103, T.104, P.105, C.132, S.163, A.164, G.165, P.166, G.167, T.168, N.171, N.290, L.291, M.294 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:I.15, 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:G.165, D:G.167, D:T.168, D:T.168, D:N.171, D:N.171, D:N.290, D:N.290 Water bridges: D:G.13, D:N.14, D:G.16, D:I.38 NAD.20: 26 residues within 4Å: Chain F: 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 F Hydrophobic interactions: F:I.15, F:M.294 Hydrogen bonds: F:S.12, F:S.12, F:N.14, F:N.14, F:I.15, F:S.42, F:T.79, F:A.81, F:G.165, F:G.167, F:T.168, F:T.168, F:N.171, F:N.171, F:N.290 Water bridges: F:S.12, F:G.13, F:N.14, F:G.16, F:I.38, F:V.60, F:V.60, F:N.87 NAD.29: 25 residues within 4Å: Chain H: 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 H Hydrophobic interactions: H:I.15, H:M.294 Hydrogen bonds: H:S.12, H:S.12, H:N.14, H:N.14, H:I.15, H:T.79, H:A.81, H:G.165, H:G.167, H:T.168, H:T.168, H:N.171, H:N.171, H:N.290 Water bridges: H:G.13, H:N.14, H:G.16, H:I.38, H:S.42, H:A.83, H: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: ACEG
acetaldehyde dehydrogenase (acylating): BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

E
A

G
C

B
F

D
H

F
B

H
D

4-hydroxy-2-oxovalerate aldolase

acetaldehyde dehydrogenase (acylating)

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