SMTL ID : 3b4w.1

Crystal structure of Mycobacterium tuberculosis aldehyde dehydrogenase complexed with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: A.235, R.238, N.457 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.457 Water bridges: A:S.234, A:A.235 Salt bridges: A:R.238 SO4.2: 4 residues within 4Å: Chain A: E.239, R.242, R.243 Chain B: R.242 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.242, A:R.243 Water bridges: A:E.239 SO4.11: 3 residues within 4Å: Chain B: A.235, R.238, N.457 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.457 Water bridges: B:S.234, B:A.235 Salt bridges: B:R.238 SO4.12: 4 residues within 4Å: Chain A: R.242 Chain B: E.239, R.242, R.243 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:E.239, B:E.239 Salt bridges: B:R.243, A:R.242

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

NAD.3: 27 residues within 4Å: Chain A: I.153, V.154, A.155, W.156, N.157, K.180, A.182, G.212, I.213, G.216, Q.217, F.230, T.231, G.232, S.233, V.236, E.239, V.240, E.254, L.255, G.256, C.288, E.387, F.389, L.415, F.452 Ligands: GOL.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.231 Hydrogen bonds: A:V.154, A:K.180, A:Q.217, A:S.233, A:E.239, A:E.239, A:L.255, A:E.387 Water bridges: A:K.180, A:A.183, A:S.234, A:E.387 NAD.13: 27 residues within 4Å: Chain B: I.153, V.154, A.155, W.156, N.157, K.180, A.182, G.212, I.213, G.216, Q.217, F.230, T.231, G.232, S.233, V.236, E.239, V.240, E.254, L.255, G.256, C.288, E.387, F.389, L.415, F.452 Ligands: GOL.16 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.231 Hydrogen bonds: B:V.154, B:K.180, B:Q.217, B:S.233, B:E.239, B:E.254, B:L.255, B:E.387 Water bridges: B:K.180, B:A.183, B:E.387, B:E.387

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.298, Y.398, D.399 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.298 GOL.5: 5 residues within 4Å: Chain A: D.302, V.305, A.306, R.352, V.354 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.302, A:D.302, A:R.352, A:R.352 Water bridges: A:D.302, A:T.309 GOL.6: 6 residues within 4Å: Chain A: N.157, V.158, F.161, G.287, C.288 Ligands: NAD.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.157, A:C.288 GOL.7: 9 residues within 4Å: Chain A: M.227, P.250, E.470, H.471, F.472, T.473, Q.474 Chain B: I.460, G.461 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.461, A:T.473 Water bridges: A:T.473, A:Q.474, A:Q.474 GOL.14: 3 residues within 4Å: Chain B: R.298, Y.398, D.399 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.298 GOL.15: 5 residues within 4Å: Chain B: D.302, V.305, A.306, R.352, V.354 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.302, B:R.352, B:R.352 Water bridges: B:D.302 GOL.16: 6 residues within 4Å: Chain B: N.157, V.158, F.161, G.287, C.288 Ligands: NAD.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.157, B:C.288 GOL.17: 9 residues within 4Å: Chain A: I.460, G.461 Chain B: M.227, P.250, E.470, H.471, F.472, T.473, Q.474 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.461, B:T.473 Water bridges: B:Q.474, B:Q.474

6 x EOH: ETHANOL(Non-functional Binders)

EOH.8: 2 residues within 4Å: Chain A: C.30, P.320 No protein-ligand interaction detected (PLIP) EOH.9: 5 residues within 4Å: Chain A: V.267, D.268, L.269, A.270, R.300 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.269, A:A.270 Hydrogen bonds: A:L.269, A:R.300, A:R.300 EOH.10: 4 residues within 4Å: Chain A: N.379, A.406, I.407, D.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 EOH.18: 2 residues within 4Å: Chain B: C.30, P.320 No protein-ligand interaction detected (PLIP) EOH.19: 5 residues within 4Å: Chain B: V.267, D.268, L.269, A.270, R.300 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.269, B:A.270 Hydrogen bonds: B:L.269, B:R.300, B:R.300 EOH.20: 4 residues within 4Å: Chain B: N.379, A.406, I.407, D.410 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.379, B:D.410

Links

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Citation

Moon, J.H. et al., X-ray crystal structure of aldehyde dehydrogenase from Mycobacterium tuberculosis complexed with NAD+. To Be Published

Release Date

2007-11-27

Peptides

Aldehyde dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aldehyde dehydrogenase