SMTL ID : 1vbi.1

Crystal structure of type 2 malate/lactate dehydrogenase from thermus thermophilus HB8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: S.43, H.44, R.48, A.179, M.180, G.181 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.181 Water bridges: A:H.44, A:R.48, A:R.48, A:D.142, A:M.180, A:K.182, A:K.182 Salt bridges: A:H.44, A:R.48 SO4.2: 2 residues within 4Å: Chain A: R.87, K.91 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.87, A:R.87, A:K.91, A:K.91 Salt bridges: A:R.87, A:K.91 SO4.3: 4 residues within 4Å: Chain A: G.269, G.273, K.274, E.275 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.274, A:E.275 Water bridges: A:G.269, A:G.273, A:A.276 SO4.9: 6 residues within 4Å: Chain B: S.43, H.44, R.48, A.179, M.180, G.181 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.181 Water bridges: B:H.44, B:R.48, B:R.48, B:M.180, B:M.180, B:K.182, B:K.182 Salt bridges: B:H.44, B:R.48 SO4.10: 2 residues within 4Å: Chain B: R.87, K.91 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.87, B:R.87, B:K.91, B:K.91 Salt bridges: B:R.87, B:K.91 SO4.11: 4 residues within 4Å: Chain B: G.269, G.273, K.274, E.275 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.274, B:E.275 Water bridges: B:G.269, B:G.273, B:A.276

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

NAD.4: 26 residues within 4Å: Chain A: H.44, H.115, F.116, G.117, M.118, A.119, T.137, A.139, T.155, P.157, V.170, A.171, D.172, L.173, A.174, K.182, F.301, P.303, G.304, L.306, E.307 Chain B: F.146, P.221, K.222, Y.224 Ligands: EDO.8 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:P.157 Hydrogen bonds: A:G.117, A:G.117, A:A.119, A:D.172, A:D.172, A:D.172, A:A.174, A:G.304, A:E.307 Water bridges: A:F.116, A:F.301, B:K.222, B:K.222, B:K.222, B:K.222 Salt bridges: A:K.182, B:K.222, B:K.222 NAD.12: 26 residues within 4Å: Chain A: F.146, P.221, K.222, Y.224 Chain B: H.44, H.115, F.116, G.117, M.118, A.119, T.137, A.139, T.155, P.157, V.170, A.171, D.172, L.173, A.174, K.182, F.301, P.303, G.304, L.306, E.307 Ligands: EDO.16 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:P.157 Hydrogen bonds: B:G.117, B:G.117, B:A.119, B:D.172, B:D.172, B:D.172, B:A.174, B:G.304, B:E.307 Water bridges: B:F.116, B:T.137, B:T.137, B:T.137, B:H.297, B:F.301, A:K.222, A:K.222, A:K.222, A:K.222 Salt bridges: B:K.182, A:K.222, A:K.222

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

EDO.5: 7 residues within 4Å: Chain A: V.144, F.146, G.147, G.148, V.199, R.216, P.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.147, A:R.216, A:R.216 EDO.6: 5 residues within 4Å: Chain A: P.68, E.70, L.77, D.79, R.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.70, A:L.77, A:R.111, A:R.111 EDO.7: 5 residues within 4Å: Chain A: E.129, G.130, F.131, D.267, K.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.267, A:K.274 EDO.8: 5 residues within 4Å: Chain A: V.41, M.118, D.172, E.307 Ligands: NAD.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.307, A:E.307 EDO.13: 7 residues within 4Å: Chain B: V.144, F.146, G.147, G.148, V.199, R.216, P.217 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.147, B:R.216, B:R.216 EDO.14: 5 residues within 4Å: Chain B: P.68, E.70, L.77, D.79, R.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.77, B:R.111, B:R.111 EDO.15: 5 residues within 4Å: Chain B: E.129, G.130, F.131, D.267, K.274 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.267, B:K.274 EDO.16: 5 residues within 4Å: Chain B: V.41, M.118, D.172, E.307 Ligands: NAD.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.307 Water bridges: B:E.307, B:E.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizutani, H. et al., Crystal structure of type 2 malate/lactate dehydrogenase from thermus thermophilus HB8. To be Published

Release Date

2005-04-19

Peptides

Type 2 malate/lactate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Type 2 malate/lactate dehydrogenase

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