SMTL ID : 6n91.1

Crystal Structure of Adenosine Deaminase from Vibrio cholerae Complexed with Pentostatin (Deoxycoformycin)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x DCF: 2'-DEOXYCOFORMYCIN(Non-covalent)

DCF.1: 17 residues within 4Å: Chain A: H.12, H.14, D.16, L.56, L.60, L.63, Y.103, I.139, S.141, A.169, G.170, H.197, E.200, H.221, D.278, D.279 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.60 Hydrogen bonds: A:D.16, A:S.100, A:G.170, A:E.200 pi-Stacking: A:H.14 DCF.8: 17 residues within 4Å: Chain B: H.12, H.14, D.16, L.56, L.60, L.63, Y.103, I.139, S.141, A.169, G.170, H.197, E.200, H.221, D.278, D.279 Ligands: ZN.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.60 Hydrogen bonds: B:D.16, B:S.100, B:G.170, B:E.200 pi-Stacking: B:H.14

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.12, H.14, H.197, H.221, D.278 Ligands: DCF.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.12, A:H.14, A:H.197, A:D.278 ZN.9: 6 residues within 4Å: Chain B: H.12, H.14, H.197, H.221, D.278 Ligands: DCF.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.12, B:H.14, B:H.197, B:D.278

3 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.3: 11 residues within 4Å: Chain A: Y.94, V.123, R.124, Q.133, A.134, N.135, L.136, H.162, L.318 Ligands: SO4.5, PO4.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.123, A:L.136 Hydrogen bonds: A:Q.133, A:A.134, A:N.135 CXS.10: 11 residues within 4Å: Chain B: Y.94, V.120, V.123, R.124, Q.133, A.134, N.135, L.136, H.162 Ligands: PO4.15, CXS.16 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.123, B:R.124, B:L.136 Hydrogen bonds: B:Q.133, B:A.134, B:N.135 CXS.16: 11 residues within 4Å: Chain B: N.135, K.160, N.161, H.162, I.163, V.164, A.190, G.191, L.192 Ligands: CXS.10, PO4.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.192 Hydrogen bonds: B:N.161

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 2 residues within 4Å: Chain A: V.112, T.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.112, A:T.113 FMT.11: 4 residues within 4Å: Chain B: I.2, T.3, S.4, S.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.4, B:S.5, B:S.5

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

SO4.5: 5 residues within 4Å: Chain A: N.135, N.161, H.162 Ligands: CXS.3, PO4.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.135, A:N.135, A:V.164

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

PO4.6: 3 residues within 4Å: Chain A: R.124 Ligands: CXS.3, SO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.162 Salt bridges: A:R.124 PO4.15: 4 residues within 4Å: Chain B: R.124, H.162 Ligands: CXS.10, CXS.16 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.124

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 1 residues within 4Å: Chain A: H.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.161 GOL.14: 5 residues within 4Å: Chain B: G.145, T.146, D.147, Q.175, R.179 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.146, B:D.147, B:D.147, B:Q.175, B:Q.175, B:R.179

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 3 residues within 4Å: Chain A: Q.48 Chain B: Q.48, I.49 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.49, A:Q.48

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 4 residues within 4Å: Chain B: P.111, V.112, T.113, Q.151 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.110, B:V.112, B:T.113, B:T.113, B:T.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal Structure of Adenosine Deaminase from Vibrio cholerae Complexed with Pentostatin (Deoxycoformycin) (CASP target). To Be Published

Release Date

2018-12-19

Peptides

Adenosine deaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenosine deaminase