SMTL ID : 2o4u.1

Crystal structure of Mammalian Dimeric Dihydrodiol Dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

14 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: S.9, V.10, A.36, R.37, R.41, Y.58 Ligands: PO4.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.10, A:G.11, A:R.37, A:Y.58, A:Y.58 Salt bridges: A:R.37, A:R.41 PO4.2: 7 residues within 4Å: Chain A: S.9, G.11, R.41, G.73, T.74, Q.75 Ligands: PO4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.9, A:S.9, A:V.10, A:R.41, A:Q.75 Water bridges: A:G.11 PO4.3: 5 residues within 4Å: Chain A: K.156, Q.233, N.236, N.251, W.254 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.233, A:N.236, A:N.251 Salt bridges: A:K.156 PO4.4: 5 residues within 4Å: Chain A: N.102, A.103, A.104, E.319, D.332 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.103, A:A.104 Water bridges: A:R.107, A:R.107 PO4.5: 6 residues within 4Å: Chain A: A.2, L.3, S.27, E.28, R.293, R.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.3, A:S.27 Salt bridges: A:R.293, A:R.297 PO4.6: 5 residues within 4Å: Chain A: D.146, R.148, T.243 Chain B: R.202, E.205 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Water bridges: B:R.202, B:E.205, A:R.148, A:R.148, A:R.148 Salt bridges: B:R.202, A:R.148 Hydrogen bonds: A:D.146, A:D.146, A:D.146 PO4.7: 7 residues within 4Å: Chain A: S.235, T.237, Q.248 Chain B: S.235, T.237, Q.248 Ligands: PO4.16 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.235, A:Q.248, A:Q.248, B:S.235, B:S.235, B:T.237, B:Q.248 Water bridges: A:T.237, A:T.237, B:Q.248 PO4.10: 7 residues within 4Å: Chain B: S.9, V.10, A.36, R.37, R.41, Y.58 Ligands: PO4.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.10, B:G.11, B:R.37, B:Y.58 Water bridges: B:Y.58 Salt bridges: B:R.37, B:R.41 PO4.11: 7 residues within 4Å: Chain B: S.9, G.11, R.41, G.73, T.74, Q.75 Ligands: PO4.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.9, B:S.9, B:V.10, B:R.41, B:Q.75 Water bridges: B:G.11 PO4.12: 5 residues within 4Å: Chain B: K.156, Q.233, N.236, N.251, W.254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.233, B:N.236, B:N.251 Salt bridges: B:K.156 PO4.13: 5 residues within 4Å: Chain B: N.102, A.103, A.104, E.319, D.332 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.103, B:A.104 Water bridges: B:R.107, B:R.107 PO4.14: 6 residues within 4Å: Chain B: A.2, L.3, S.27, E.28, R.293, R.297 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.2, B:L.3, B:S.27 Salt bridges: B:R.293, B:R.297 PO4.15: 5 residues within 4Å: Chain A: R.202, E.205 Chain B: D.146, R.148, T.243 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Water bridges: A:R.202, A:E.205, B:R.148, B:R.148, B:R.148 Salt bridges: A:R.202, B:R.148 Hydrogen bonds: B:D.146, B:D.146 PO4.16: 7 residues within 4Å: Chain A: S.235, T.237, Q.248 Chain B: S.235, T.237, Q.248 Ligands: PO4.7 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.235, A:S.235, A:Q.248, B:S.235, B:T.237, B:Q.248, B:Q.248 Water bridges: A:T.237, A:T.237, A:Q.248

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.8: 8 residues within 4Å: Chain A: A.152, Y.180, C.181, Q.183, F.184, A.238, C.253, W.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.183 Water bridges: A:C.253 BME.17: 8 residues within 4Å: Chain B: A.152, Y.180, C.181, Q.183, F.184, A.238, C.253, W.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.183 Water bridges: B:C.253

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: F.154, K.156, L.158, L.177, W.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.156, A:W.254 Water bridges: A:R.163 GOL.18: 5 residues within 4Å: Chain B: F.154, K.156, L.158, L.177, W.254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.156, B:W.254 Water bridges: B:R.163, B:Y.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carbone, V. et al., Structures of dimeric dihydrodiol dehydrogenase apoenzyme and inhibitor complex: probing the subunit interface with site-directed mutagenesis. Proteins (2008)

Release Date

2007-07-31

Peptides

Dimeric dihydrodiol dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

Dimeric dihydrodiol dehydrogenase

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