SMTL ID : 2jbh.1

Human phosphoribosyl transferase domain containing 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: L.75, K.76, G.77, D.201, R.207 Ligands: CA.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:L.75, A:K.76, A:G.77 Water bridges: A:G.78, A:D.201, A:R.207, A:R.207, A:R.207, A:R.207, A:R.207 Salt bridges: A:R.207 PO4.5: 6 residues within 4Å: Chain B: L.75, K.76, G.77, D.201, R.207 Ligands: CA.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.76, B:G.77 Water bridges: B:G.78, B:R.108, B:D.201, B:R.207, B:R.207, B:R.207, B:R.207, B:R.207 Salt bridges: B:R.207 PO4.9: 6 residues within 4Å: Chain C: L.75, K.76, G.77, D.201, R.207 Ligands: CA.11 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:L.75, C:K.76, C:G.77 Water bridges: C:G.78, C:D.201, C:R.207, C:R.207, C:R.207, C:R.207, C:R.207 Salt bridges: C:R.207 PO4.13: 6 residues within 4Å: Chain D: L.75, K.76, G.77, D.201, R.207 Ligands: CA.14 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.76, D:G.77 Water bridges: D:G.78, D:R.108, D:D.142, D:D.201, D:R.207, D:R.207, D:R.207, D:R.207 Salt bridges: D:R.207

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.141, D.142 Ligands: 5GP.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.141, A:D.142, H2O.6, H2O.6, H2O.6 CA.3: 2 residues within 4Å: Chain A: D.201 Ligands: PO4.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.201, H2O.5, H2O.5, H2O.6 CA.6: 2 residues within 4Å: Chain B: D.201 Ligands: PO4.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.201, H2O.11, H2O.11, H2O.12, H2O.12 CA.7: 3 residues within 4Å: Chain B: E.141, D.142 Ligands: 5GP.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.141, B:D.142, H2O.12, H2O.12, H2O.12 CA.10: 3 residues within 4Å: Chain C: E.141, D.142 Ligands: 5GP.12 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.141, C:D.142, H2O.18, H2O.18, H2O.18 CA.11: 2 residues within 4Å: Chain C: D.201 Ligands: PO4.9 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.201, H2O.17, H2O.17, H2O.18 CA.14: 2 residues within 4Å: Chain D: D.201 Ligands: PO4.13 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.201, H2O.23, H2O.23, H2O.23, H2O.23 CA.15: 3 residues within 4Å: Chain D: E.141, D.142 Ligands: 5GP.16 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.141, D:D.142, H2O.23, H2O.23, H2O.24

4 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.4: 16 residues within 4Å: Chain A: E.141, D.142, V.143, V.144, G.145, T.146, G.147, R.148, T.149, K.173, L.193, F.194, V.195, L.200, D.201 Ligands: CA.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.141, A:V.143, A:G.145, A:T.146, A:T.146, A:T.146, A:G.147, A:R.148, A:T.149, A:T.149, A:K.173, A:V.195, A:V.195, A:V.195, A:D.201 Water bridges: A:R.148, A:R.148, A:T.149, A:M.150 Salt bridges: A:D.142 5GP.8: 16 residues within 4Å: Chain B: E.141, D.142, V.143, V.144, G.145, T.146, G.147, R.148, T.149, K.173, L.193, F.194, V.195, L.200, D.201 Ligands: CA.7 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:V.143, B:V.143, B:G.145, B:T.146, B:T.146, B:T.146, B:G.147, B:R.148, B:T.149, B:T.149, B:K.173, B:V.195, B:V.195, B:V.195, B:D.201 Water bridges: B:T.146, B:T.146, B:T.146, B:T.149, B:M.150 Salt bridges: B:D.142 5GP.12: 16 residues within 4Å: Chain C: E.141, D.142, V.143, V.144, G.145, T.146, G.147, R.148, T.149, K.173, L.193, F.194, V.195, L.200, D.201 Ligands: CA.10 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:E.141, C:V.143, C:G.145, C:T.146, C:T.146, C:T.146, C:G.147, C:R.148, C:T.149, C:T.149, C:K.173, C:V.195, C:V.195, C:V.195, C:D.201 Water bridges: C:E.141, C:T.146, C:T.146, C:R.148, C:R.148, C:T.149, C:M.150 Salt bridges: C:D.142 5GP.16: 16 residues within 4Å: Chain D: E.141, D.142, V.143, V.144, G.145, T.146, G.147, R.148, T.149, K.173, L.193, F.194, V.195, L.200, D.201 Ligands: CA.15 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:E.141, D:V.143, D:G.145, D:T.146, D:T.146, D:T.146, D:G.147, D:R.148, D:T.149, D:T.149, D:K.173, D:V.195, D:V.195, D:D.201, D:D.201 Water bridges: D:E.141, D:D.142, D:D.142, D:T.149, D:M.150 Salt bridges: D:D.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Welin, M. et al., Structural and Functional Studies of the Human Phosphoribosyltransferase Domain Containing Protein 1. FEBS J. (2010)

Release Date

2006-12-20

Peptides

PHOSPHORIBOSYLTRANSFERASE DOMAIN-CONTAINING PROTEIN 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PHOSPHORIBOSYLTRANSFERASE DOMAIN-CONTAINING PROTEIN 1