SMTL ID : 6qaf.1 (1 other biounit)

Crystal structure of human Arginase-1 at pH 9.0 in complex with CB-1158/INCB001158

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-trimer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: H.121, D.144, D.148, D.252 Ligands: MN.2, XC3.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.121, A:D.144, A:D.148, A:D.252 MN.2: 7 residues within 4Å: Chain A: D.144, H.146, D.252, D.254 Ligands: MN.1, XC3.3, NA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.144, A:H.146, A:D.252, A:D.254, A:D.254 MN.5: 6 residues within 4Å: Chain B: H.121, D.144, D.148, D.252 Ligands: MN.6, XC3.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.121, B:D.144, B:D.148, B:D.252 MN.6: 7 residues within 4Å: Chain B: D.144, H.146, D.252, D.254 Ligands: MN.5, XC3.7, NA.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.144, B:H.146, B:D.252, B:D.254, B:D.254 MN.9: 6 residues within 4Å: Chain C: H.121, D.144, D.148, D.252 Ligands: MN.10, XC3.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.121, C:D.144, C:D.148, C:D.252 MN.10: 7 residues within 4Å: Chain C: D.144, H.146, D.252, D.254 Ligands: MN.9, XC3.11, NA.12 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.144, C:H.146, C:D.252, C:D.254, C:D.254

3 x XC3: [(~{E})-3-[(3~{S},4~{R})-4-azanyl-1-[(2~{S})-2-azanylpropanoyl]-4-carboxy-pyrrolidin-3-yl]prop-1-enyl]-tris(oxidanyl)boranium(Non-covalent)

XC3.3: 18 residues within 4Å: Chain A: H.121, D.144, H.146, D.148, N.150, S.157, H.161, G.162, D.201, D.203, E.206, D.252, D.254, T.266, E.297 Ligands: MN.1, MN.2, NA.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.150, A:S.157, A:D.203, A:T.266, A:T.266 Water bridges: A:D.148, A:T.155, A:T.155, A:S.157, A:S.157, A:N.159, A:H.161, A:G.162, A:D.201, A:D.203 XC3.7: 18 residues within 4Å: Chain B: H.121, D.144, H.146, D.148, N.150, S.157, H.161, G.162, D.201, D.203, E.206, D.252, D.254, T.266, E.297 Ligands: MN.5, MN.6, NA.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:N.150, B:S.157, B:D.203, B:T.266, B:T.266 Water bridges: B:D.148, B:T.155, B:T.155, B:S.157, B:S.157, B:N.159, B:H.161, B:G.162, B:D.201, B:D.203 XC3.11: 18 residues within 4Å: Chain C: H.121, D.144, H.146, D.148, N.150, S.157, H.161, G.162, D.201, D.203, E.206, D.252, D.254, T.266, E.297 Ligands: MN.9, MN.10, NA.12 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:N.150, C:S.157, C:D.203, C:T.266, C:T.266 Water bridges: C:D.148, C:T.155, C:T.155, C:S.157, C:S.157, C:N.159, C:H.161, C:G.162, C:D.201, C:D.203

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

NA.4: 6 residues within 4Å: Chain A: D.252, D.254, T.266, E.297 Ligands: MN.2, XC3.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.266 Water bridges: A:G.265 NA.8: 6 residues within 4Å: Chain B: D.252, D.254, T.266, E.297 Ligands: MN.6, XC3.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.297 Water bridges: B:G.265 NA.12: 6 residues within 4Å: Chain C: D.252, D.254, T.266, E.297 Ligands: MN.10, XC3.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.297 Water bridges: C:G.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grobben, Y. et al., Structural insights into human Arginase-1 pH dependence and its inhibition by the small molecule inhibitor CB-1158. J Struct Biol X (2020)

Release Date

2019-12-11

Peptides

Arginase-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Arginase-1

Related Entries With Identical Sequence