SMTL ID : 9bbo.2 (2 other biounits)

Proline utilization A complexed with the product L-glutamate in the aldehyde dehydrogenase active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x GGL: GAMMA-L-GLUTAMIC ACID(Non-covalent)

GGL.1: 10 residues within 4Å: Chain A: N.709, F.710, I.714, R.845, C.846, S.847, I.1003, G.1004, A.1005, F.1012 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.710, A:I.714, A:F.1012, A:F.1012 Hydrogen bonds: A:N.709, A:C.846, A:S.847, A:G.1004, A:A.1005 Water bridges: A:E.676, A:E.676, A:A.1005, A:A.1005 Salt bridges: A:R.845 GGL.9: 10 residues within 4Å: Chain B: N.709, F.710, I.714, R.845, C.846, S.847, I.1003, G.1004, A.1005, F.1012 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.710, B:I.714, B:F.1012, B:F.1012 Hydrogen bonds: B:N.709, B:C.846, B:S.847, B:G.1004, B:A.1005 Water bridges: B:E.676, B:E.676, B:E.676, B:A.1005, B:A.1005 Salt bridges: B:R.845

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: R.690, P.1041, Q.1042 Chain B: S.96, Q.98, E.99, A.169, R.172 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Q.1042, B:S.96 Water bridges: A:R.690, A:R.690, B:S.96, B:S.97, B:R.172, B:R.172 Salt bridges: A:R.690, B:R.172 SO4.3: 6 residues within 4Å: Chain A: S.139, Q.855, E.856, D.857, R.954, R.955 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.139, A:Q.855, A:D.857, A:R.955 Salt bridges: A:R.954 SO4.4: 5 residues within 4Å: Chain A: L.157, T.158, S.159, R.1093, A.1229 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.159, A:S.159 Water bridges: A:L.157, A:A.1229, A:A.1229 Salt bridges: A:R.1093 SO4.5: 3 residues within 4Å: Chain A: S.1196, G.1198, R.1202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.1196, A:G.1198 Salt bridges: A:R.1202 SO4.6: 2 residues within 4Å: Chain A: K.1062, K.1141 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.1062 SO4.10: 8 residues within 4Å: Chain A: S.96, Q.98, E.99, A.169, R.172 Chain B: R.690, P.1041, Q.1042 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Q.1042, A:S.96, A:S.96 Water bridges: B:R.690, B:Q.1042, A:S.97, A:S.165, A:S.165, A:R.172 Salt bridges: B:R.690, A:R.172 SO4.11: 5 residues within 4Å: Chain B: L.157, T.158, S.159, R.1093, A.1229 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.159, B:S.159 Water bridges: B:A.1229 Salt bridges: B:R.1093 SO4.12: 6 residues within 4Å: Chain B: S.139, Q.855, E.856, D.857, R.954, R.955 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.855, B:D.857, B:R.955 Water bridges: B:D.956 Salt bridges: B:R.954 SO4.13: 3 residues within 4Å: Chain B: R.805, S.1196, R.1202 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.1196 Water bridges: B:R.805, B:R.1202 Salt bridges: B:R.805, B:R.1202

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 5 residues within 4Å: Chain A: L.1080, G.1081, L.1082, L.1098, H.1099 No protein-ligand interaction detected (PLIP) PGE.15: 5 residues within 4Å: Chain B: L.1080, G.1081, L.1082, L.1098, H.1099 No protein-ligand interaction detected (PLIP)

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.8: 32 residues within 4Å: Chain A: D.308, A.309, V.340, Q.342, Y.344, R.369, V.371, K.372, G.373, A.374, Y.375, W.376, F.394, T.395, R.396, K.397, T.400, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, E.494, N.495, S.499, S.500, F.501, I.1234, G.1235 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:A.423, A:Q.449, A:Y.475, A:Y.475 Hydrogen bonds: A:A.309, A:A.309, A:Q.342, A:R.369, A:K.372, A:G.373, A:G.373, A:G.373, A:A.374, A:T.395, A:K.397, A:T.400, A:T.424, A:H.425, A:H.425, A:N.426, A:E.494, A:S.499, A:F.501 Water bridges: A:K.267, A:A.423, A:V.502 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376 FAD.16: 32 residues within 4Å: Chain B: D.308, A.309, V.340, Q.342, Y.344, R.369, V.371, K.372, G.373, A.374, Y.375, W.376, F.394, T.395, R.396, K.397, T.400, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, E.494, N.495, S.499, S.500, F.501, I.1234, G.1235 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:A.423, B:Q.449, B:Y.475 Hydrogen bonds: B:A.309, B:A.309, B:Q.342, B:R.369, B:K.372, B:G.373, B:G.373, B:G.373, B:A.374, B:T.395, B:H.425, B:N.426, B:E.494, B:S.499, B:F.501, B:G.1235 Water bridges: B:A.423, B:E.494, B:V.502 Salt bridges: B:K.372, B:K.372, B:K.397 pi-Stacking: B:W.376, B:W.376

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 6 residues within 4Å: Chain B: G.544, D.545, A.546, R.547, T.548, R.689 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.544 Water bridges: B:T.548

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buckley, D.B. et al., Visualization of transient states and molecular motions in the catalytic cycle of the proline catabolic bifunctional enzyme Proline Utilization A from kinetic crystallography and molecular dynamics simulations. To Be Published

Release Date

2025-03-12

Peptides

Trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

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