X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a urea based inhibitor PSMA 1007
Barinka, C., Novakova, Z., Motlova, L.To be published.
Experimental Data Snapshot
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutamate carboxypeptidase 2 | 707 | Homo sapiens | Mutation(s): 0  Gene Names: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 EC: 3.4.17.21 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q04609 (Homo sapiens) Explore Q04609  Go to UniProtKB:  Q04609 | |||||
PHAROS:  Q04609 GTEx:  ENSG00000086205  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q04609 | ||||
Glycosylation | |||||
Glycosylation Sites: 7 | Go to GlyGen: Q04609-1 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 3 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 4 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Ligands 5 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
9OT Query on 9OT | M [auth A] | (2~{S})-2-[[(2~{S})-6-[[(2~{S})-2-[[4-[[[(2~{S})-2-[[(2~{S})-2-[(6-fluoranylpyridin-3-yl)carbonylamino]-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]methyl]phenyl]carbonylamino]-3-naphthalen-2-yl-propanoyl]amino]-1-oxidanyl-1-oxidanylidene-hexan-2-yl]carbamoylamino]pentanedioic acid C49 H55 F N8 O16 RFFFFGRYVZESLB-LTLCPEALSA-N | |||
NAG Query on NAG | E [auth A], F [auth A], G [auth A], H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | I [auth A], J [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | K [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | L [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 101.657 | α = 90 |
b = 130.159 | β = 90 |
c = 159.16 | γ = 90 |
Software Name | Purpose |
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REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
Coot | model building |