SMTL ID : 1u7h.1

Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: A.224, V.225, G.226, G.227, S.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.227, A:G.227, A:S.293 NA.6: 5 residues within 4Å: Chain B: A.224, V.225, G.226, G.227, S.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.224, B:G.227, B:S.293

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

NAD.2: 27 residues within 4Å: Chain A: T.78, T.84, V.85, R.112, T.113, I.135, G.136, G.138, A.139, Q.140, Y.160, D.161, T.162, D.163, A.166, V.201, T.202, A.203, I.210, V.225, G.226, D.228, K.232, S.293, V.294, G.295 Chain B: K.331 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.113, A:Q.140, A:V.225 Hydrogen bonds: A:R.112, A:A.139, A:Q.140, A:Q.140, A:T.162, A:T.162, A:T.202, A:A.203, A:V.225, A:K.232, B:K.331, B:K.331 Water bridges: A:T.78, A:T.84, A:T.84, A:T.84, A:T.84, A:T.84, A:R.112, A:G.138, A:S.141, A:D.204, A:D.204, A:K.232, A:S.293 NAD.7: 26 residues within 4Å: Chain A: K.331 Chain B: T.78, T.84, V.85, R.112, T.113, G.136, G.138, A.139, Q.140, Y.160, D.161, T.162, D.163, A.166, V.201, T.202, A.203, I.210, V.225, G.226, D.228, K.232, S.293, V.294, G.295 28 PLIP interactions: 2 interactions with chain A, 26 interactions with chain B Hydrogen bonds: A:K.331, A:K.331, B:R.112, B:A.139, B:Q.140, B:Q.140, B:T.162, B:T.162, B:T.202, B:A.203, B:V.225, B:K.232 Hydrophobic interactions: B:T.113, B:Q.140, B:V.225 Water bridges: B:T.78, B:T.84, B:T.84, B:T.84, B:T.84, B:T.84, B:R.112, B:G.138, B:S.141, B:D.204, B:D.204, B:K.232, B:S.293

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 7 residues within 4Å: Chain A: Q.38, A.39, F.40, D.41, A.61, D.62, K.63 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.41 Hydrogen bonds: A:K.63 MPD.4: 2 residues within 4Å: Chain A: Q.38, A.39 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.39 MPD.5: 5 residues within 4Å: Chain A: Y.3, A.311, E.312, G.315, M.316 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.3 MPD.8: 7 residues within 4Å: Chain B: S.64, R.65, L.91, A.92, D.93, V.100, L.308 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.91, B:V.100 Water bridges: B:V.94 MPD.9: 5 residues within 4Å: Chain B: Y.3, A.311, E.312, G.315, M.316 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.3, B:E.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goodman, J.L. et al., Ornithine Cyclodeaminase: Structure, Mechanism of Action, and Implications forthe u-Crystallin Family;. Biochemistry (2004)

Release Date

2004-11-09

Peptides

ornithine cyclodeaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ornithine cyclodeaminase

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