SMTL ID : 1guy.1

Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: I.8, G.9, A.10, G.11, F.12, V.13, D.33, I.34, V.35, Y.65, T.77, S.78, G.79, I.98, C.102, V.118, N.119, N.120, L.147, H.175, A.225, P.229 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.13, A:P.229 Hydrogen bonds: A:A.10, A:F.12, A:V.13, A:I.34, A:Y.65, A:G.79, A:N.119, A:N.120, A:H.175 Water bridges: A:A.10, A:G.11, A:G.14, A:K.42, A:A.80, A:A.80, A:N.120, A:R.151, A:R.151 NAD.5: 26 residues within 4Å: Chain B: I.8, G.9, A.10, G.11, F.12, V.13, L.32, D.33, I.34, V.35, Y.65, T.77, S.78, G.79, A.80, I.98, C.102, V.118, N.119, N.120, Q.143, L.147, H.175, S.224, A.225, P.229 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.13, B:P.229 Hydrogen bonds: B:A.10, B:F.12, B:V.13, B:I.34, B:G.79, B:N.120, B:N.120, B:Q.143, B:H.175 Water bridges: B:G.11, B:G.14, B:A.80, B:R.151, B:R.151 NAD.8: 22 residues within 4Å: Chain C: I.8, G.9, A.10, G.11, F.12, V.13, D.33, I.34, V.35, Y.65, T.77, S.78, G.79, I.98, C.102, V.118, N.119, N.120, L.147, H.175, A.225, P.229 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:V.13, C:P.229 Hydrogen bonds: C:A.10, C:F.12, C:V.13, C:I.34, C:G.79, C:N.119, C:N.120, C:H.175 Water bridges: C:A.10, C:G.11, C:G.14, C:K.42, C:A.80, C:A.80, C:N.120, C:R.151, C:R.151 NAD.12: 26 residues within 4Å: Chain D: I.8, G.9, A.10, G.11, F.12, V.13, L.32, D.33, I.34, V.35, Y.65, T.77, S.78, G.79, A.80, I.98, C.102, V.118, N.119, N.120, Q.143, L.147, H.175, S.224, A.225, P.229 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.13, D:P.229 Hydrogen bonds: D:A.10, D:F.12, D:V.13, D:I.34, D:Y.65, D:G.79, D:N.120, D:N.120, D:Q.143, D:H.175 Water bridges: D:G.11, D:G.14, D:A.80, D:R.151, D:R.151

10 x CD: CADMIUM ION(Non-covalent)

CD.2: 1 residues within 4Å: Chain A: E.165 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.165, A:E.165, H2O.11, H2O.13 CD.3: 1 residues within 4Å: Chain A: E.281 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.281, A:E.281 CD.4: 1 residues within 4Å: Chain A: D.200 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.200, A:D.200 CD.6: 1 residues within 4Å: Chain B: E.165 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.165, B:E.165, H2O.5, H2O.5 CD.7: 1 residues within 4Å: Chain B: E.159 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.159, B:E.159, H2O.10 CD.9: 1 residues within 4Å: Chain C: E.165 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.165, C:E.165, H2O.1, H2O.23 CD.10: 1 residues within 4Å: Chain C: E.281 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.281, C:E.281 CD.11: 1 residues within 4Å: Chain C: D.200 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.200, C:D.200 CD.13: 1 residues within 4Å: Chain D: E.165 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.165, D:E.165, H2O.17, H2O.17 CD.14: 1 residues within 4Å: Chain D: E.159 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.159, D:E.159, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dalhus, B. et al., Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases. J.Mol.Biol. (2002)

Release Date

2002-02-15

Peptides

MALATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

MALATE DEHYDROGENASE

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