SMTL ID : 4lvc.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

3 x ADN: ADENOSINE(Non-covalent)

ADN.1: 19 residues within 4Å: Chain A: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, H.348, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.68, A:T.69, A:T.204, A:K.233, A:K.233, A:H.348, A:H.398 ADN.7: 19 residues within 4Å: Chain B: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, H.348, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:T.204, B:T.204, B:K.233, B:K.233, B:H.348, B:H.398 ADN.16: 19 residues within 4Å: Chain C: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, H.348, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.18 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.68, C:E.203, C:T.204, C:K.233, C:K.233, C:H.348, C:H.398

3 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.2: 6 residues within 4Å: Chain A: Q.68, M.396, G.397, H.398, P.399 Chain C: D.255 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Water bridges: C:D.255, A:Q.94 Hydrogen bonds: A:Q.68, A:G.397 NH4.8: 6 residues within 4Å: Chain B: Q.68, M.396, G.397, H.398, P.399 Chain D: D.255 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.398 Water bridges: B:Q.94, B:S.400 NH4.17: 5 residues within 4Å: Chain C: Q.68, M.396, G.397, H.398, P.399 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.68, C:M.396 Water bridges: C:Q.94, A:D.255

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

NAD.3: 30 residues within 4Å: Chain A: T.204, T.205, T.206, N.238, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398 Chain B: L.456, Q.460, I.464, K.473, Y.477 Ligands: ADN.1 26 PLIP interactions: 21 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.271 Hydrogen bonds: A:T.205, A:T.205, A:T.206, A:T.206, A:N.238, A:G.269, A:D.270, A:V.271, A:V.291, A:D.292, A:N.325, A:H.348, A:N.391, A:N.391, B:Q.460, B:K.473, B:K.473, B:Y.477, B:Y.477 Water bridges: A:D.270, A:D.270, A:G.272, A:S.289, A:F.349, A:E.352 NAD.9: 29 residues within 4Å: Chain A: L.456, Q.460, K.473, Y.477 Chain B: T.204, T.205, T.206, D.237, N.238, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, N.391, H.398 Ligands: ADN.7 25 PLIP interactions: 20 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.271 Hydrogen bonds: B:T.205, B:T.205, B:T.206, B:T.206, B:T.206, B:N.238, B:G.269, B:D.270, B:V.271, B:V.291, B:D.292, B:N.325, B:H.348, B:N.391, B:N.391, A:Q.460, A:Q.460, A:K.473, A:K.473 Water bridges: B:D.270, B:D.270, B:G.272, B:S.289, A:R.457 NAD.18: 30 residues within 4Å: Chain C: T.204, T.205, T.206, D.237, N.238, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398 Chain D: L.456, Q.460, K.473, Y.477 Ligands: ADN.16 25 PLIP interactions: 19 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:V.271 Hydrogen bonds: C:T.205, C:T.206, C:T.206, C:N.238, C:D.270, C:V.271, C:V.291, C:D.292, C:N.325, C:H.348, C:N.391, C:N.391, D:Q.460, D:K.473, D:K.473, D:Y.477, D:Y.477 Water bridges: C:N.228, C:G.269, C:G.272, C:S.289, C:F.349, C:E.352, D:Q.460 NAD.24: 28 residues within 4Å: Chain C: L.456, Q.460, I.464, K.473, Y.477 Chain D: D.237, N.238, C.242, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398 20 PLIP interactions: 6 interactions with chain C, 14 interactions with chain D Hydrogen bonds: C:Q.460, C:K.473, C:K.473, C:Y.477, C:Y.477, D:G.269, D:D.270, D:V.271, D:V.291, D:D.292, D:N.325, D:N.391, D:N.391 Water bridges: C:Q.460, D:N.238, D:N.238, D:G.272, D:S.289, D:H.348 Hydrophobic interactions: D:V.271

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: T.205, T.206, H.209, G.324 Chain B: Y.463, I.464 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.463 GOL.5: 6 residues within 4Å: Chain A: V.432, L.433, K.435, D.438, D.475 Chain B: R.478 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.435, A:D.438, A:D.438, A:D.475, B:R.478 GOL.6: 5 residues within 4Å: Chain A: K.112, R.252, G.393, N.394, A.395 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.112, A:K.112, A:R.252, A:N.394 GOL.10: 7 residues within 4Å: Chain A: R.478 Chain B: V.432, L.433, P.434, K.435, D.438, D.475 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.435, B:D.438, B:D.438, B:D.475, A:R.478 Water bridges: B:K.435 GOL.11: 4 residues within 4Å: Chain B: P.39, M.42, A.43, E.46 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.39, B:E.46 Water bridges: B:E.46, B:E.46 GOL.12: 6 residues within 4Å: Chain B: K.112, R.252, G.393, N.394, A.395, M.396 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.112, B:K.112, B:R.252, B:N.394 GOL.13: 9 residues within 4Å: Chain B: G.260, R.285 Chain C: A.300, Y.304, E.305, V.306 Chain D: I.449, G.450, V.451 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:V.306, C:V.306, B:G.260, B:R.285, D:G.450 GOL.19: 7 residues within 4Å: Chain C: V.231, V.432, L.433, K.435, D.438, D.475 Chain D: R.478 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.435, C:K.435, C:D.438, C:D.475, D:R.478 Water bridges: D:R.478 GOL.20: 6 residues within 4Å: Chain C: K.112, R.252, G.393, N.394, A.395, M.396 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.112, C:K.112, C:R.252 Water bridges: A:R.252 GOL.21: 6 residues within 4Å: Chain B: R.280, G.303 Chain C: R.280, G.283, C.284, R.285 9 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:R.280, B:G.303, C:R.280 Water bridges: B:E.302, B:E.302, C:R.280, C:G.283, C:V.286, A:Q.281 GOL.22: 6 residues within 4Å: Chain C: G.465, V.466, P.471, Y.472, K.473, S.474 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.465 Water bridges: C:K.467, C:Y.472 GOL.25: 5 residues within 4Å: Chain D: V.432, L.433, K.435, D.438, D.475 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Water bridges: C:R.478, D:K.435 Hydrogen bonds: D:K.435, D:K.435, D:D.438, D:D.475 GOL.26: 7 residues within 4Å: Chain D: C.88, N.89, I.90, L.116, Y.119, D.144, E.170 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:C.88, D:I.90, D:E.170 GOL.27: 5 residues within 4Å: Chain C: E.302 Chain D: L.239, R.243, K.273, A.277 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Water bridges: C:E.302, C:E.302 Hydrogen bonds: D:R.243, D:R.243 GOL.28: 2 residues within 4Å: Chain D: K.458, D.462 No protein-ligand interaction detected (PLIP)

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.14: 4 residues within 4Å: Chain B: K.112, G.113, P.368, Q.369 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.112, B:P.368 Hydrogen bonds: B:Q.369, B:Q.369 ACT.15: 4 residues within 4Å: Chain B: G.465, P.471, K.473, S.474 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.473 ACT.23: 5 residues within 4Å: Chain C: D.350, I.355, A.356, R.359, R.388 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.355, C:A.356, C:R.359 Water bridges: C:I.355, C:I.355, C:R.388, C:R.388 Salt bridges: C:R.359, C:R.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manszewski, T. et al., An enzyme captured in two conformational states: crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii. Acta Crystallogr.,Sect.D (2015)

Release Date

2014-07-30

Peptides

S-adenosyl-L-homocysteine hydrolase (SAHase): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

S-adenosyl-L-homocysteine hydrolase (SAHase)

Related Entries With Identical Sequence