SMTL ID : 1x7d.1

Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 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:V.225, A:G.227, A:S.293 NA.9: 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:V.225, B:G.227, B:S.293

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

NAD.2: 28 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 Ligands: ORN.3 29 PLIP interactions: 27 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:V.85, A:G.138, A:S.141, A:D.204, A:D.204, A:D.204, A:D.204, A:K.232, A:S.293 NAD.10: 27 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 Ligands: ORN.4 27 PLIP interactions: 25 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.113, B:Q.140, B:V.225 Hydrogen bonds: 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, A:K.331, A:K.331 Water bridges: B:T.78, B:T.84, B:T.84, B:T.84, B:T.84, B:T.84, B:G.138, B:S.141, B:D.204, B:D.204, B:K.232, B:S.293

2 x ORN: L-ornithine(Non-covalent)

ORN.3: 14 residues within 4Å: Chain A: R.45, V.54, E.56, M.58, K.69, V.71, N.72, G.73, T.109, R.112, D.228, V.294, G.295 Ligands: NAD.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.71 Hydrogen bonds: A:R.45, A:R.45, A:G.73, A:D.228 Salt bridges: A:R.45, A:K.69, A:R.112 ORN.4: 14 residues within 4Å: Chain B: R.45, E.56, M.58, K.69, V.71, N.72, G.73, V.85, T.109, R.112, D.228, V.294, G.295 Ligands: NAD.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.71 Hydrogen bonds: B:R.45, B:R.45, B:N.72, B:D.228 Salt bridges: B:R.45, B:K.69, B:R.112

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

MPD.5: 8 residues within 4Å: Chain A: Q.38, A.39, F.40, D.41, A.61, D.62, K.63 Ligands: MPD.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.63 MPD.6: 3 residues within 4Å: Chain A: Q.38, A.39 Ligands: MPD.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.39 MPD.7: 6 residues within 4Å: Chain A: S.64, R.65, L.91, D.93, V.100, L.308 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.65, A:L.91, A:V.100, A:L.308 Hydrogen bonds: A:D.93 MPD.8: 6 residues within 4Å: Chain A: Y.3, L.308, A.311, E.312, G.315, M.316 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.3, A:Y.3, A:L.308 MPD.12: 6 residues within 4Å: Chain B: Y.3, L.308, A.311, E.312, G.315, M.316 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.3, B:L.308, B:E.312 MPD.13: 7 residues within 4Å: Chain B: S.64, R.65, L.91, A.92, D.93, V.100, L.308 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.94

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.11: 4 residues within 4Å: Chain A: R.338 Chain B: H.15, E.176, Y.177 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:H.15, A:R.338 Salt bridges: B:H.15, B:E.176, A:R.338

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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