SMTL ID : 1uxj.1

Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: 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, P.81, I.98, C.102, V.118, N.119, N.120, L.122, Q.143, L.147, H.175, A.225, P.229 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.118, A:L.147, A:P.229 Hydrogen bonds: A:F.12, A:V.13, A:I.34, A:Y.65, A:G.79, A:V.118, A:N.120, A:N.120, A:Q.143 Water bridges: A:A.10, A:G.11, A:G.14, A:K.42 NAD.9: 28 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, L.122, Q.143, A.144, L.147, H.175, S.224, A.225, P.229 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.118, B:L.147, B:P.229 Hydrogen bonds: B:A.10, B:F.12, B:V.13, B:I.34, B:G.79, B:V.118, B:N.120, B:N.120, B:Q.143 Water bridges: B:G.11, B:G.14 NAD.17: 27 residues within 4Å: Chain C: 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, P.81, I.98, C.102, V.118, N.119, N.120, L.122, Q.143, L.147, H.175, A.225, P.229 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:V.118, C:L.147, C:P.229 Hydrogen bonds: C:F.12, C:V.13, C:I.34, C:G.79, C:V.118, C:N.120, C:N.120, C:Q.143 Water bridges: C:A.10, C:G.11, C:G.14, C:K.42 NAD.25: 28 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, L.122, Q.143, A.144, L.147, H.175, S.224, A.225, P.229 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.118, D:L.147, D:P.229 Hydrogen bonds: D:A.10, D:F.12, D:V.13, D:I.34, D:Y.65, D:G.79, D:V.118, D:N.120, D:N.120, D:Q.143 Water bridges: D:G.11, D:G.14

18 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.2: 2 residues within 4Å: Chain A: D.243, E.277 Ligand excluded by PLIP CD.3: 2 residues within 4Å: Chain A: E.195 Chain B: E.281 Ligand excluded by PLIP CD.4: 2 residues within 4Å: Chain A: E.178 Ligands: CL.6 Ligand excluded by PLIP CD.5: 2 residues within 4Å: Chain A: D.148, H.175 Ligand excluded by PLIP CD.10: 2 residues within 4Å: Chain B: E.178 Ligands: CL.13 Ligand excluded by PLIP CD.11: 2 residues within 4Å: Chain B: E.159, R.201 Ligand excluded by PLIP CD.12: 2 residues within 4Å: Chain B: D.148, H.175 Ligand excluded by PLIP CD.15: 1 residues within 4Å: Chain C: E.238 Ligand excluded by PLIP CD.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.18: 2 residues within 4Å: Chain C: D.243, E.277 Ligand excluded by PLIP CD.19: 2 residues within 4Å: Chain C: E.195 Chain D: E.281 Ligand excluded by PLIP CD.20: 2 residues within 4Å: Chain C: E.178 Ligands: CL.22 Ligand excluded by PLIP CD.21: 2 residues within 4Å: Chain C: D.148, H.175 Ligand excluded by PLIP CD.26: 2 residues within 4Å: Chain D: E.178 Ligands: CL.29 Ligand excluded by PLIP CD.27: 2 residues within 4Å: Chain D: E.159, R.201 Ligand excluded by PLIP CD.28: 2 residues within 4Å: Chain D: D.148, H.175 Ligand excluded by PLIP CD.31: 1 residues within 4Å: Chain A: E.238 Ligand excluded by PLIP CD.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: P.121, D.123, A.124, T.302 Ligands: CD.4 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: P.121, D.123, A.124, T.302 Ligands: CD.10 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain C: P.121, D.123, A.124, T.302 Ligands: CD.20 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain D: P.121, D.123, A.124, T.302 Ligands: CD.26 Ligand excluded by PLIP

6 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain A: H.19, Y.227 Chain C: H.19, Y.227 Ligands: NA.23 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.19, C:H.19 NA.8: 3 residues within 4Å: Chain A: Y.226 Chain C: Y.226 Ligands: NA.24 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:Y.226, C:Y.227, A:Y.227, A:Y.227 NA.14: 2 residues within 4Å: Chain A: K.165 Chain B: E.238 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.165 NA.23: 5 residues within 4Å: Chain A: H.19, Y.227 Chain C: H.19, Y.227 Ligands: NA.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.19, C:H.19 NA.24: 3 residues within 4Å: Chain A: Y.226 Chain C: Y.226 Ligands: NA.8 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Water bridges: A:S.15, A:Y.227, C:S.15, C:Y.226, C:Y.227, C:Y.227 NA.30: 2 residues within 4Å: Chain C: K.165 Chain D: E.238 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bjork, A. et al., Large Improvement in the Thermal Stability of a Tetrameric Malate Dehydrogenase by Single Point Mutations at the Dimer-Dimer Interface. J.Mol.Biol. (2004)

Release Date

2004-08-26

Peptides

MALATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

MALATE DEHYDROGENASE

Related Entries With Identical Sequence