SMTL ID : 3rfv.1

Crystal structure of Uronate dehydrogenase from Agrobacterium tumefaciens complexed with NADH and product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 27 residues within 4Å: Chain A: G.10, A.12, G.13, Q.14, L.15, D.34, L.35, S.36, C.50, D.51, L.52, L.71, G.72, G.73, I.74, S.75, G.86, A.109, S.110, S.111, Y.136, K.140, I.163, G.164, S.165, C.166 Ligands: 15L.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.163, A:I.163 Hydrogen bonds: A:Q.14, A:L.15, A:L.35, A:S.36, A:D.51, A:L.52, A:L.71, A:G.73, A:I.74, A:S.75, A:Y.136, A:K.140, A:C.166 Water bridges: A:G.13, A:Q.14, A:G.16, A:S.36, A:S.36, A:S.75, A:V.76, A:C.166 NAI.7: 27 residues within 4Å: Chain B: G.10, A.12, G.13, Q.14, L.15, D.34, L.35, S.36, C.50, D.51, L.52, L.71, G.72, G.73, I.74, S.75, G.86, A.109, S.110, S.111, Y.136, K.140, I.163, G.164, S.165, C.166 Ligands: 15L.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.163, B:I.163 Hydrogen bonds: B:G.10, B:Q.14, B:L.15, B:L.35, B:S.36, B:D.51, B:D.51, B:L.52, B:L.71, B:G.73, B:I.74, B:S.75, B:Y.136, B:K.140, B:C.166, B:C.166 Water bridges: B:G.13, B:G.16, B:S.36, B:V.76, B:G.86, B:G.86 NAI.11: 27 residues within 4Å: Chain C: G.10, A.12, G.13, Q.14, L.15, D.34, L.35, S.36, C.50, D.51, L.52, L.71, G.72, G.73, I.74, S.75, G.86, A.109, S.110, S.111, Y.136, K.140, I.163, G.164, S.165, C.166 Ligands: 15L.12 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:I.163, C:I.163 Hydrogen bonds: C:Q.14, C:L.15, C:L.35, C:S.36, C:D.51, C:D.51, C:L.52, C:L.71, C:G.73, C:I.74, C:S.75, C:Y.136, C:K.140, C:C.166, C:C.166 Water bridges: C:G.13, C:G.16, C:S.36, C:S.36, C:V.76, C:G.86 NAI.15: 27 residues within 4Å: Chain D: G.10, A.12, G.13, Q.14, L.15, D.34, L.35, S.36, C.50, D.51, L.52, L.71, G.72, G.73, I.74, S.75, G.86, A.109, S.110, S.111, Y.136, K.140, I.163, G.164, S.165, C.166 Ligands: 15L.16 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.163, D:I.163 Hydrogen bonds: D:Q.14, D:L.15, D:L.35, D:S.36, D:D.51, D:D.51, D:L.52, D:L.71, D:G.73, D:I.74, D:S.75, D:K.140, D:C.166 Water bridges: D:G.13, D:Q.14, D:G.16, D:S.36, D:S.36, D:S.75, D:V.76, D:C.166 NAI.21: 27 residues within 4Å: Chain E: G.10, A.12, G.13, Q.14, L.15, D.34, L.35, S.36, C.50, D.51, L.52, L.71, G.72, G.73, I.74, S.75, G.86, A.109, S.110, S.111, Y.136, K.140, I.163, G.164, S.165, C.166 Ligands: 15L.22 22 PLIP interactions: 22 interactions with chain E Hydrophobic interactions: E:I.163, E:I.163 Hydrogen bonds: E:G.10, E:Q.14, E:L.15, E:L.35, E:S.36, E:D.51, E:L.52, E:L.71, E:G.73, E:I.74, E:S.75, E:K.140, E:C.166, E:C.166 Water bridges: E:G.13, E:G.16, E:S.36, E:V.76, E:G.86, E:G.86 NAI.25: 27 residues within 4Å: Chain F: G.10, A.12, G.13, Q.14, L.15, D.34, L.35, S.36, C.50, D.51, L.52, L.71, G.72, G.73, I.74, S.75, G.86, A.109, S.110, S.111, Y.136, K.140, I.163, G.164, S.165, C.166 Ligands: 15L.26 21 PLIP interactions: 21 interactions with chain F Hydrophobic interactions: F:I.163, F:I.163 Hydrogen bonds: F:Q.14, F:L.15, F:L.35, F:S.36, F:D.51, F:L.52, F:L.71, F:G.73, F:I.74, F:S.75, F:K.140, F:C.166, F:C.166 Water bridges: F:G.13, F:G.16, F:S.36, F:S.36, F:V.76, F:G.86

6 x 15L: D-galactaro-1,5-lactone(Non-covalent)

15L.2: 10 residues within 4Å: Chain A: S.75, S.111, N.112, H.113, Y.136, G.164, S.165, R.174, F.258 Ligands: NAI.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.111, A:N.112, A:Y.136 Water bridges: A:Q.14, A:S.75, A:C.166 Salt bridges: A:H.113, A:H.113, A:R.174 15L.8: 10 residues within 4Å: Chain B: S.75, S.111, N.112, H.113, Y.136, G.164, S.165, R.174, F.258 Ligands: NAI.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.111, B:N.112, B:N.112, B:Y.136 Water bridges: B:S.75 Salt bridges: B:H.113, B:H.113, B:R.174 15L.12: 10 residues within 4Å: Chain C: S.75, S.111, N.112, H.113, Y.136, G.164, S.165, R.174, F.258 Ligands: NAI.11 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.111, C:N.112, C:N.112, C:Y.136 Water bridges: C:Q.14, C:S.75, C:S.75, C:C.166 Salt bridges: C:H.113, C:H.113, C:R.174 15L.16: 10 residues within 4Å: Chain D: S.75, S.111, N.112, H.113, Y.136, G.164, S.165, R.174, F.258 Ligands: NAI.15 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.111, D:N.112, D:Y.136, D:Y.136 Water bridges: D:Q.14, D:S.75, D:C.166 Salt bridges: D:H.113, D:H.113, D:R.174 15L.22: 10 residues within 4Å: Chain E: S.75, S.111, N.112, H.113, Y.136, G.164, S.165, R.174, F.258 Ligands: NAI.21 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:S.111, E:N.112, E:N.112, E:Y.136, E:Y.136 Water bridges: E:S.75 Salt bridges: E:H.113, E:H.113, E:R.174 15L.26: 10 residues within 4Å: Chain F: S.75, S.111, N.112, H.113, Y.136, G.164, S.165, R.174, F.258 Ligands: NAI.25 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:S.111, F:N.112, F:N.112, F:Y.136, F:Y.136 Water bridges: F:Q.14, F:S.75, F:S.75, F:C.166 Salt bridges: F:H.113, F:H.113, F:R.174

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

PO4.3: 3 residues within 4Å: Chain A: G.64, A.100, H.101 Ligand excluded by PLIP PO4.4: 4 residues within 4Å: Chain A: V.18, E.21, R.22, H.182 Ligand excluded by PLIP PO4.5: 4 residues within 4Å: Chain A: R.123, G.125, D.215 Chain F: H.218 Ligand excluded by PLIP PO4.6: 2 residues within 4Å: Chain A: P.119, R.131 Ligand excluded by PLIP PO4.9: 4 residues within 4Å: Chain B: A.63, G.64, H.101, G.102 Ligand excluded by PLIP PO4.10: 3 residues within 4Å: Chain B: K.265 Chain C: A.55, Y.92 Ligand excluded by PLIP PO4.13: 4 residues within 4Å: Chain C: A.63, G.64, H.101, G.102 Ligand excluded by PLIP PO4.14: 2 residues within 4Å: Chain C: R.22, H.182 Ligand excluded by PLIP PO4.17: 3 residues within 4Å: Chain D: G.64, A.100, H.101 Ligand excluded by PLIP PO4.18: 4 residues within 4Å: Chain D: V.18, E.21, R.22, H.182 Ligand excluded by PLIP PO4.19: 4 residues within 4Å: Chain C: H.218 Chain D: R.123, G.125, D.215 Ligand excluded by PLIP PO4.20: 2 residues within 4Å: Chain D: P.119, R.131 Ligand excluded by PLIP PO4.23: 4 residues within 4Å: Chain E: A.63, G.64, H.101, G.102 Ligand excluded by PLIP PO4.24: 3 residues within 4Å: Chain E: K.265 Chain F: A.55, Y.92 Ligand excluded by PLIP PO4.27: 4 residues within 4Å: Chain F: A.63, G.64, H.101, G.102 Ligand excluded by PLIP PO4.28: 2 residues within 4Å: Chain F: R.22, H.182 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parkkinen, T. et al., Crystal Structure of Uronate Dehydrogenase from Agrobacterium tumefaciens. J.Biol.Chem. (2011)

Release Date

2011-06-15

Peptides

Uronate dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Uronate dehydrogenase

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