SMTL ID : 1ur5.1

Stabilization of a Tetrameric Malate Dehydrogenase by Introduction of a Disulfide Bridge 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: 26 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, 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 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:N.119, A:N.120, A:Q.143, A:H.175 Water bridges: A:A.10, A:G.11, A:G.14, A:K.42, A:R.151, A:R.151 NAD.7: 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, N.95, I.98, C.102, V.118, N.119, N.120, L.147, H.175, S.224, A.225, P.229 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.13, B:P.229 Hydrogen bonds: B:F.12, B:V.13, B:I.34, B:G.79, B:N.120, B:N.120, B:H.175 Water bridges: B:G.11, B:G.14, B:R.151, B:R.151 NAD.12: 26 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, 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 C Hydrophobic interactions: C:V.13, C:P.229 Hydrogen bonds: C:A.10, C:F.12, C:V.13, C:I.34, C:N.119, C:N.120, C:Q.143, C:H.175 Water bridges: C:A.10, C:G.11, C:G.14, C:K.42, C:R.151, C:R.151 NAD.18: 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, N.95, I.98, C.102, V.118, N.119, N.120, L.147, H.175, S.224, A.225, P.229 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:V.13, D:P.229 Hydrogen bonds: D:F.12, D:V.13, D:I.34, D:Y.65, D:G.79, D:N.120, D:N.120, D:H.175 Water bridges: D:G.11, D:G.14, D:R.151, D:R.151

12 x CD: CADMIUM ION(Non-covalent)

CD.2: 2 residues within 4Å: Chain A: E.178 Ligands: CL.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.178, H2O.6, H2O.7 CD.3: 1 residues within 4Å: Chain A: E.165 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.165, A:E.165, H2O.19 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.8: 1 residues within 4Å: Chain B: E.178 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.178, H2O.15, H2O.16, H2O.16 CD.9: 1 residues within 4Å: Chain B: E.165 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.165, B:E.165, H2O.9 CD.10: 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.17 CD.13: 2 residues within 4Å: Chain C: E.178 Ligands: CL.16 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.178, H2O.28, H2O.28 CD.14: 1 residues within 4Å: Chain C: E.165 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.165, C:E.165, H2O.40 CD.15: 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.19: 1 residues within 4Å: Chain D: E.178 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.178, H2O.36, H2O.37, H2O.37 CD.20: 1 residues within 4Å: Chain D: E.165 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.165, D:E.165, H2O.30 CD.21: 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.38

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

CL.5: 5 residues within 4Å: Chain A: P.121, D.123, A.124, T.302 Ligands: CD.2 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain C: P.121, D.123, A.124, T.302 Ligands: CD.13 Ligand excluded by PLIP

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

NA.6: 3 residues within 4Å: Chain A: H.19 Chain C: H.19 Ligands: NA.17 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:H.19 Water bridges: A:T.16, A:H.19, A:Y.227, A:Y.227, C:T.16, C:Y.227 NA.11: 3 residues within 4Å: Chain B: H.19 Chain D: H.19 Ligands: NA.22 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Water bridges: B:T.16, B:Y.227, D:T.16, D:Y.227 Hydrogen bonds: D:H.19 NA.17: 3 residues within 4Å: Chain A: H.19 Chain C: H.19 Ligands: NA.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.19, C:H.19 Water bridges: A:Y.227 NA.22: 3 residues within 4Å: Chain B: H.19 Chain D: H.19 Ligands: NA.11 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:H.19 Water bridges: D:T.16, D:Y.227, B:T.16, B:Y.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bjork, A. et al., Stabilization of a Tetrameric Malate Dehydrogenase by Introduction of a Disulfide Bridge at the Dimer-Dimer Interface. J.Mol.Biol. (2003)

Release Date

2003-11-05

Peptides

MALATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

MALATE DEHYDROGENASE