SMTL ID : 8cfh.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment C08

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385 Chain D: Q.453, K.466, Y.470 Ligands: ADE.2, PO4.6 24 PLIP interactions: 19 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:V.235 Hydrogen bonds: A:T.169, A:T.170, A:T.170, A:N.202, A:G.233, A:D.234, A:V.235, A:V.255, A:D.256, A:N.303, A:H.326, A:N.378, A:N.378, D:Q.453, D:Q.453, D:K.466, D:K.466, D:Y.470 Water bridges: A:D.234, A:D.234, A:G.236, A:F.327, A:E.330 NAD.10: 33 residues within 4Å: Chain B: T.168, T.169, T.170, D.201, N.202, C.206, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385 Chain C: L.449, Q.453, K.466, Y.470 Ligands: ADE.11, PO4.15 25 PLIP interactions: 20 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:N.202, B:V.235 Hydrogen bonds: B:T.169, B:T.170, B:T.170, B:N.202, B:G.233, B:D.234, B:V.235, B:V.255, B:D.256, B:N.303, B:H.326, B:N.378, B:N.378, C:Q.453, C:Q.453, C:K.466, C:K.466, C:Y.470 Water bridges: B:T.169, B:D.234, B:G.236, B:F.327, B:E.330 NAD.19: 32 residues within 4Å: Chain B: L.449, Q.453, K.466, Y.470 Chain C: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385 Ligands: ADE.20, PO4.23 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:V.235 Hydrogen bonds: C:T.169, C:T.169, C:T.170, C:T.170, C:T.170, C:N.202, C:G.233, C:D.234, C:V.235, C:V.255, C:D.256, C:N.303, C:H.326, C:N.378, C:N.378, B:Q.453, B:Q.453, B:K.466, B:K.466 Water bridges: C:T.169, C:D.234, C:G.236, C:F.327, C:E.330 NAD.28: 32 residues within 4Å: Chain A: L.449, Q.453, K.466, Y.470 Chain D: T.168, T.169, T.170, D.201, N.202, I.230, G.231, G.233, D.234, V.235, A.253, E.254, V.255, D.256, C.259, T.300, T.301, G.302, N.303, V.306, I.324, G.325, H.326, L.376, N.378, H.385 Ligands: ADE.29, PO4.34 27 PLIP interactions: 22 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:N.202, D:V.235 Hydrogen bonds: D:T.169, D:T.169, D:T.169, D:T.170, D:T.170, D:N.202, D:G.233, D:D.234, D:V.235, D:V.255, D:D.256, D:N.303, D:H.326, D:N.378, D:N.378, A:Q.453, A:Q.453, A:K.466, A:K.466, A:Y.470 Water bridges: D:D.234, D:D.234, D:G.236, D:F.327, D:E.330

4 x ADE: ADENINE(Non-covalent)

ADE.2: 12 residues within 4Å: Chain A: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.1, PO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.68, A:T.69, A:H.385 ADE.11: 12 residues within 4Å: Chain B: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.10, PO4.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.68, B:H.385 ADE.20: 12 residues within 4Å: Chain C: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.19, PO4.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.66, C:Q.68, C:H.385 ADE.29: 12 residues within 4Å: Chain D: H.64, T.66, Q.68, T.69, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.28, PO4.34 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:T.69, D:H.385

4 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: Q.68, T.383, G.384, H.385 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.383, A:T.383, A:H.385, H2O.6, H2O.11 K.12: 4 residues within 4Å: Chain B: Q.68, T.383, G.384, H.385 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.383, B:T.383, B:H.385, H2O.23, H2O.26 K.21: 5 residues within 4Å: Chain C: Q.68, T.383, G.384, H.385, P.386 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.383, C:T.383, C:H.385, H2O.37, H2O.42 K.31: 4 residues within 4Å: Chain D: Q.68, T.383, G.384, H.385 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.383, D:T.383, D:H.385, H2O.56, H2O.57

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

PO4.4: 6 residues within 4Å: Chain A: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.5: 4 residues within 4Å: Chain A: R.28, I.32, E.35 Chain B: H.363 Ligand excluded by PLIP PO4.6: 10 residues within 4Å: Chain A: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.1, ADE.2 Ligand excluded by PLIP PO4.13: 4 residues within 4Å: Chain A: H.363 Chain B: R.28, I.32, E.35 Ligand excluded by PLIP PO4.14: 6 residues within 4Å: Chain B: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.15: 10 residues within 4Å: Chain B: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.10, ADE.11 Ligand excluded by PLIP PO4.16: 6 residues within 4Å: Chain B: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP PO4.22: 4 residues within 4Å: Chain C: R.28, I.32, E.35 Chain D: H.363 Ligand excluded by PLIP PO4.23: 10 residues within 4Å: Chain C: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.19, ADE.20 Ligand excluded by PLIP PO4.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.25: 6 residues within 4Å: Chain C: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP PO4.26: 6 residues within 4Å: Chain C: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.32: 6 residues within 4Å: Chain D: K.313, A.314, L.315, K.316, K.317, R.354 Ligand excluded by PLIP PO4.33: 4 residues within 4Å: Chain C: H.363 Chain D: R.28, I.32, E.35 Ligand excluded by PLIP PO4.34: 10 residues within 4Å: Chain D: H.64, D.142, E.167, T.168, K.197, D.201, H.385, M.390 Ligands: NAD.28, ADE.29 Ligand excluded by PLIP PO4.35: 6 residues within 4Å: Chain D: G.458, V.459, P.464, F.465, K.466, P.467 Ligand excluded by PLIP

7 x R8V: (3S)-3-hydroxy-2-methyl-2,3-dihydro-1H-isoindol-1-one(Non-covalent)

R8V.7: 9 residues within 4Å: Chain A: P.467, T.469, Y.470, R.471 Chain D: L.176, N.190, D.193, V.425 Ligands: R8V.9 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:D.193, D:V.425 Hydrogen bonds: D:N.190, A:T.469 R8V.8: 7 residues within 4Å: Chain A: K.429, L.436, Q.448, V.461, E.462, F.465 Chain D: P.257 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.448, A:E.462 Hydrogen bonds: A:K.429 R8V.9: 10 residues within 4Å: Chain A: D.468, T.469, Y.470, R.471 Chain D: D.468, T.469, Y.470, R.471 Ligands: R8V.7, R8V.36 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:T.469, A:R.471 Hydrogen bonds: D:R.471, D:R.471 R8V.17: 9 residues within 4Å: Chain B: P.467, T.469, Y.470, R.471 Chain C: L.176, N.190, D.193, V.425 Ligands: R8V.18 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:D.193, C:V.425 Hydrogen bonds: C:N.190, B:T.469 R8V.18: 10 residues within 4Å: Chain B: D.468, T.469, Y.470, R.471 Chain C: D.468, T.469, Y.470, R.471 Ligands: R8V.17, R8V.27 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.471 Hydrophobic interactions: B:T.469, B:R.471 R8V.27: 9 residues within 4Å: Chain B: L.176, N.190, D.193, V.425 Chain C: P.467, T.469, Y.470, R.471 Ligands: R8V.18 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:T.469, B:D.193, B:V.425 Hydrogen bonds: C:T.469, B:N.190 R8V.36: 9 residues within 4Å: Chain A: L.176, N.190, D.193, V.425 Chain D: P.467, T.469, Y.470, R.471 Ligands: R8V.9 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:D.193, A:V.425 Hydrogen bonds: A:N.190, A:D.193, D:T.469

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.30: 3 residues within 4Å: Chain D: A.418, K.419, L.421 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry C08. To be published

Release Date

2024-02-21

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase

Related Entries With Identical Sequence