SMTL ID : 6vua.2 (1 other biounit)

X-ray structure of human CD38 catalytic domain with 2'-Cl-araNAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x ROJ: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R})-4-chloranyl-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate(Covalent)

ROJ.1: 14 residues within 4Å: Chain A: W.82, S.83, R.84, K.86, E.103, D.112, D.113, S.143, W.146, S.150, S.177, T.178, F.179, E.183 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.84, A:K.86, A:E.103, A:D.112, A:D.112, A:D.113, A:T.178, A:T.178, A:T.178, A:F.179 Water bridges: A:W.82, A:R.84, A:E.103, A:L.114, A:K.147 Salt bridges: A:R.84, A:R.84 pi-Stacking: A:W.146, A:W.146, A:W.146

1 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: P.189, V.192, N.227 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:P.189, A:V.192, A:N.227, H2O.3, H2O.7

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

PO4.3: 2 residues within 4Å: Chain A: R.169, S.170 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.170 Water bridges: A:S.168, A:S.168, A:R.169, A:S.170, A:S.170, A:S.170, A:K.171 Salt bridges: A:R.169

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 7 residues within 4Å: Chain A: M.67, G.70, T.71, Q.72, T.105, R.152, F.153 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.72 Hydrogen bonds: A:Q.72, A:Q.72 MPD.5: 8 residues within 4Å: Chain A: H.31, Q.72, V.74, P.75, R.97, D.98, F.100, D.104 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.74, A:P.75 Hydrogen bonds: A:H.31 Water bridges: A:M.99, A:D.104

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

PEG.6: 7 residues within 4Å: Chain A: Q.6, W.7, S.8, G.9, P.10, Q.128, S.129 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.8, A:G.11 PEG.7: 5 residues within 4Å: Chain A: P.17, Q.40, W.43, D.44, K.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.40, A:K.47 PEG.8: 2 residues within 4Å: Chain A: T.13, K.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, Z. et al., Synthesis of site-specific antibody-drug conjugates by ADP-ribosyl cyclases. Sci Adv (2020)

Release Date

2020-06-03

Peptides

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1

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